diff --git a/docs/404.html b/docs/404.html index bfd4e54a15..52ea5fbc73 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,7 @@ Page not found (404) • scCustomize - + @@ -18,7 +18,7 @@ - +
@@ -47,7 +47,7 @@
  • @@ -127,7 +133,7 @@
    • - +
    @@ -155,16 +161,16 @@

    Page not found (404)

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 808898af0b..7891d2884a 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -1,9 +1,9 @@ -GNU General Public License • scCustomizeGNU General Public License • scCustomize - +
    @@ -31,7 +31,7 @@
    • - +
    @@ -321,15 +327,15 @@

    How to Apply These Terms

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/Cell_Bender_Functions.html b/docs/articles/Cell_Bender_Functions.html index 4d6c4fdeb1..c6fb03cec8 100644 --- a/docs/articles/Cell_Bender_Functions.html +++ b/docs/articles/Cell_Bender_Functions.html @@ -6,20 +6,19 @@ Cell Bender Functionality & Plotting • scCustomize - + - - +
    @@ -48,7 +47,7 @@
  • @@ -128,7 +133,7 @@
    • - +
    @@ -136,7 +141,7 @@

    Cell Bender Functionality & Plotting

    -

    Compiled: February 28, +

    Compiled: December 05, 2024

    Source: vignettes/articles/Cell_Bender_Functions.Rmd @@ -171,7 +176,7 @@

    CellBender Functionalitylibrary(viridis) library(Seurat) library(scCustomize) -library(qs)

    +library(qs)

    Importing Cell Bender H5 Outputs

    @@ -293,7 +298,7 @@

    Create Seurat Object with Co

    Creating a Seurat object from merged CellBender matrices then is identical to creating any other Seurat object.

    -cell_bender_seurat <- CreateSeuratObject(counts = cell_bender_merged, names.field = 1, names.delim = "_")
    +cell_bender_seurat <- CreateSeuratObject(counts = cell_bender_merged, names.field = 1, names.delim = "_")

    Creating Dual Assay Objects @@ -330,7 +335,7 @@

    Create Dual Assay Seurat ObjectOptional Parameters

    Users can specify any additional parameters normally passed to -Seurat::CreateSeuratObject() when using this function.

    +Seurat::CreateSeuratObject() when using this function.

     dual_seurat <- Create_CellBender_Merged_Seurat(raw_cell_bender_matrix = cell_bender_merged, raw_counts_matrix = cell_ranger_merged,
     raw_assay_name = "RAW", min_cells = 5, min_features = 200)
    @@ -785,15 +790,20 @@
    Non-Ambient RNA gene

    +
    +

    Optional Parameters +

    +

    FeaturePlot_DualAssay also contains optional parameter +(colors_use_assay2) that allows for returning plots with +different color palettes for each assay.

    +
    + @@ -806,16 +816,16 @@
    Non-Ambient RNA gene

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-17-1.png b/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-17-1.png index 2899e75465..0feabbf148 100644 Binary files a/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-17-1.png and b/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-17-1.png differ diff --git a/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-19-1.png b/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-19-1.png index b17c8d3b41..8c62bcaad1 100644 Binary files a/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-19-1.png and b/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-19-1.png differ diff --git a/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-22-1.png b/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-22-1.png new file mode 100644 index 0000000000..28cd685cb8 Binary files /dev/null and b/docs/articles/Cell_Bender_Functions_files/figure-html/unnamed-chunk-22-1.png differ diff --git a/docs/articles/Color_Palettes.html b/docs/articles/Color_Palettes.html index 4ad200b987..6f379313d4 100644 --- a/docs/articles/Color_Palettes.html +++ b/docs/articles/Color_Palettes.html @@ -6,20 +6,19 @@ Customized Color Palettes & Themes • scCustomize - + - - +
    @@ -48,7 +47,7 @@
  • @@ -128,14 +133,14 @@
    • - +

    Customized Color Palettes & Themes

    -

    Compiled: February 28, +

    Compiled: December 05, 2024

    Source: vignettes/articles/Color_Palettes.Rmd @@ -169,7 +174,7 @@

    Choosing Color Palettes and Themeslibrary(magrittr) library(patchwork) library(scCustomize) -library(qs) +library(qs) # Load Marsh et al., 2022 datasets marsh_mouse_micro <- qread(file = "assets/marsh_2020_micro.qs") @@ -383,9 +388,7 @@

    Suggestions/Enhancements? - -

    +
    @@ -398,16 +401,16 @@

    Suggestions/Enhancements?

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/Color_Palettes_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/Color_Palettes_files/figure-html/unnamed-chunk-10-1.png index 66b749cf1e..c66f2eaf27 100644 Binary files a/docs/articles/Color_Palettes_files/figure-html/unnamed-chunk-10-1.png and b/docs/articles/Color_Palettes_files/figure-html/unnamed-chunk-10-1.png differ diff --git a/docs/articles/Color_Palettes_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/Color_Palettes_files/figure-html/unnamed-chunk-12-1.png index 650525697c..df443016ca 100644 Binary files a/docs/articles/Color_Palettes_files/figure-html/unnamed-chunk-12-1.png and b/docs/articles/Color_Palettes_files/figure-html/unnamed-chunk-12-1.png differ diff --git a/docs/articles/Color_Palettes_files/figure-html/unnamed-chunk-12-2.png b/docs/articles/Color_Palettes_files/figure-html/unnamed-chunk-12-2.png index ab2fd531b1..7c6bfe451c 100644 Binary files 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b/docs/articles/FAQ.html @@ -6,20 +6,19 @@ Frequently Asked Questions • scCustomize - + - - +
    @@ -48,7 +47,7 @@
  • @@ -128,14 +133,14 @@
    • - +

    Frequently Asked Questions

    -

    Compiled: February 28, +

    Compiled: December 05, 2024

    Source: vignettes/articles/FAQ.Rmd @@ -245,16 +250,16 @@

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/Gene_Expression_Plotting.html b/docs/articles/Gene_Expression_Plotting.html index 2b4536b6b2..3f773da34a 100644 --- a/docs/articles/Gene_Expression_Plotting.html +++ b/docs/articles/Gene_Expression_Plotting.html @@ -6,20 +6,19 @@ Plotting #1: Analysis Plots • scCustomize - + - - +
    @@ -48,7 +47,7 @@
  • @@ -128,14 +133,15 @@
    • - -
    + + +

    Plotting #1: Analysis Plots

    -

    Compiled: February 28, +

    Compiled: December 05, 2024

    Source: vignettes/articles/Gene_Expression_Plotting.Rmd @@ -176,7 +182,7 @@

    Customizing Plot library(viridis) library(Seurat) library(scCustomize) -library(qs) +library(qs) # Load Marsh et al., 2022 datasets marsh_mouse_micro <- qread(file = "assets/marsh_2020_micro.qs") @@ -723,29 +729,38 @@

    Cluster Plot on Gene Expressio 
     Clustered_DotPlot(seurat_object = pbmc, features = top_markers, k = 8)

    +

    You can also change the location and orientation of the plot legends. +For instance here we move the legend to the bottom of the plot and +reorient the legend to display horizontally. We also remove the identity +legend as redundant information (and it takes up a lot of room when +horizontal).

    +
    +plots <- Clustered_DotPlot(seurat_object = pbmc, features = top_markers, k = 8, plot_km_elbow = FALSE,
+    legend_position = "bottom", legend_orientation = "horizontal", show_ident_legend = FALSE)
    +

    Clustered_DotPlot() split by additional grouping variable

    Clustered_DotPlot can now plot with additional grouping variable provided to split.by parameter.

    -
    +
     Clustered_DotPlot(seurat_object = marsh_mouse_micro, features = c("Fos", "Jun", "Egr1", "Aif1",
     "P2ry12", "Tmem119"), split.by = "Transcription_Method")
    
-
    
+
    
 
    However, you’ll notice that the labels on the bottom get cutoff on
 the left-hand side of the plot. There are two solutions to this.
    
 
    Keep bottom labels rotated but add extra white-space padding on
 left
    
-
    +
     Clustered_DotPlot(seurat_object = marsh_mouse_micro, features = c("Fos", "Jun", "Egr1", "Aif1",
     "P2ry12", "Tmem119"), split.by = "Transcription_Method", plot_padding = TRUE)
    
-
    
+
    
 
    Or simply remove the bottom label text rotation
    
-
    +
     Clustered_DotPlot(seurat_object = marsh_mouse_micro, features = c("Fos", "Jun", "Egr1", "Aif1",
     "P2ry12", "Tmem119"), split.by = "Transcription_Method", x_lab_rotate = 90)
    
-
    
+
    
 
    
 
    
 
    Clustered_DotPlot() k-means Clustering Optional Parameters
@@ -756,8 +771,15 @@ 
    Clustered_DotP
 the elbow in sum of squares error plot. By default
 Clustered_DotPlot will return this plot when using the
 function. However, it can be turned off by setting
-plot_km_elbow = FALSE.
-
    
+plot_km_elbow = FALSE.
    
+
    +plots <- Clustered_DotPlot(seurat_object = pbmc, features = top_markers, k = 8, plot_km_elbow = TRUE,
+    legend_position = "bottom", legend_orientation = "horizontal", show_ident_legend = FALSE)
+
+plots[[1]]
    
+
    +plots[[1]]
    
+
    
 
    The number of k values plotted must be 1 less than number of
 features. Default is to plot 20 values but users can customize number of
 k values plotted using elbow_kmax parameter.
    
@@ -789,18 +811,18 @@ 
    Clustered_DotPlo
 of exp_color_min/exp_color_max but can be
 modified if a skewed visualization is desired.
 
-
    +
     Clustered_DotPlot(seurat_object = pbmc, features = top_markers, k = 8, print_exp_quantiles = T)
    
-
    Quantiles of gene expression data are:
-       10%        50%        90%        99% 
--0.6555988 -0.3595223  1.7742718  2.6666597
    
+
    Quantiles of gene expression data are:
+       10%        50%        90%        99% 
+-0.6555988 -0.3595223  1.7742718  2.6666597
    
 
    Here we can adjust the expression clipping based on the range of the
 data in this specific dataset and list of features and change the color
 scale to use Seurat::PurpleAndYellow()
    
-
    +
     Clustered_DotPlot(seurat_object = pbmc, features = top_markers, k = 8, exp_color_min = -1, exp_color_max = 2,
     colors_use_exp = PurpleAndYellow())
    
-
    
+
    
 
    
 
    
 
    Clustered_DotPlot() Other Optional Parameters
@@ -811,6 +833,11 @@ 
    Clustered_DotPlot() Other O
 (columns) plotted.
    
 
 
  • 
+show_ident_colors and show_ident_legend to
+show or hide the identity colors on plot and/or identity legend. Default
+is TRUE.
    
+
    • 
+
  • 
 x_lab_rotate Logical or Integer. Default is TRUE (45
 degree column label rotation). FALSE (0 degree rotation). Integer for
 custom text rotation value.
    
@@ -820,6 +847,15 @@ 
    Clustered_DotPlot() Other O
 symbols).
    
 
    • 
 
  • 
+show_row_names and show_column_names to
+show or hide the column and row names. Default is TRUE.
    • 
+
  • 
+column_names_side and row_names_side to
+change the location of column and row labels. Default is
+column_names_side = "bottom" and
+row_names_side = "right".
    
+
    • 
+
  • 
 raster Whether to rasterize the plot (faster and
 smaller file size). Default is FALSE.
    • 
 
@@ -835,11 +871,11 @@ 
    FeatureScater Plots
    +
     # Create Plots
 FeatureScatter_scCustom(seurat_object = marsh_mouse_micro, feature1 = "exAM_Score1", feature2 = "Microglia_Score1",
     colors_use = mouse_colors, group.by = "ident", num_columns = 2, pt.size = 1)
    
-
    
+
    
 
    
 
    Split FeatureScatter Plots
 
    
@@ -852,12 +888,752 @@ 
    Split FeatureScatter PlotsDimPlot_scCustom. The default
 is to return each plot with their own x and y axes, which has a number
 of advantages (see DimPlot_scCustom section).
    
-
    +
     # Create Plots
 FeatureScatter_scCustom(seurat_object = marsh_mouse_micro, feature1 = "exAM_Score1", feature2 = "Microglia_Score1",
     colors_use = mouse_colors, split.by = "Transcription_Method", group.by = "ident", num_columns = 2,
     pt.size = 1)
    
-
    
+
    
+
    
+
    
+
    
+
    Heatmaps
+
    
+
    While scCustomize does not have a custom heatmap plot itself (yet…)
+it does have functions that can make cell-level heatmaps easier to
+view/interpret. By default the heatmap in Seurat will size the groups on
+the heatmap based om their size in the dataset. This can make it very
+hard to view the results (especially for small clusters).
    
+
    +# Selection fo cluster marker genes
+micro_markers <- c("P2ry12", "Cx3cr1", "Fos", "Hspa1a", "Ms4a7", "Ccr2", "Isg15", "Ifit3", "Lpl",
+    "Plaur", "Mki67", "Top2a")
+
+DoHeatmap(object = marsh_mouse_micro, features = micro_markers)
    
+
    +# Selection fo cluster marker genes
+micro_markers <- c("P2ry12", "Cx3cr1", "Fos", "Hspa1a", "Ms4a7", "Ccr2", "Isg15", "Ifit3", "Lpl",
+    "Plaur", "Mki67", "Top2a")
+
+
+marsh_mouse_micro2 <- ScaleData(marsh_mouse_micro, features = micro_markers)
+
+
+DoHeatmap(object = marsh_mouse_micro2, features = micro_markers)
    
+
    
+*Very hard to view the results for anything but the Homeostatic and activated clusters*
    
+Very hard to view the results for anything but the Homeostatic and
+activated clusters
+
    
+
    
+
    While this can be helpful in someways to gauge cluster size other
+visualizations are usually better for that and heatmaps are usually
+aimed at informing relative (scaled) gene expression across clusters,
+groups, etc.
    
+
    We can solve this issue by downsampling which cells are used in the
+plot so that number of cells is equal across all groups.
    
+
    First we need to get idea of how many cells are in each identity.
+scCustomize provides the Cluster_Stats_All_Samples function
+to make this easy.
    
+
    +cluster_stats <- Cluster_Stats_All_Samples(seurat_object = marsh_mouse_micro)
+
+cluster_stats
    
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
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+
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+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
    
+Cluster
+
+Number
+
+Freq
+
+1
+
+2
+
+3
+
+4
+
+5
+
+6
+
+7
+
+8
+
+9
+
+10
+
+11
+
+12
+
+1_%
+
+2_%
+
+3_%
+
+4_%
+
+5_%
+
+6_%
+
+7_%
+
+8_%
+
+9_%
+
+10_%
+
+11_%
+
+12_%
+
    
+Homeostatic
+
+15993
+
+81.7512651
+
+1518
+
+930
+
+1552
+
+1323
+
+912
+
+728
+
+1931
+
+1609
+
+1441
+
+429
+
+2087
+
+1533
+
+79.2275574
+
+57.0202330
+
+95.0980392
+
+92.2594142
+
+92.0282543
+
+61.904762
+
+94.6568627
+
+96.0597015
+
+94.3062827
+
+24.6551724
+
+94.4771390
+
+96.3544940
+
    
+Activated
+
+2670
+
+13.6482135
+
+293
+
+651
+
+14
+
+46
+
+3
+
+402
+
+16
+
+4
+
+5
+
+1220
+
+12
+
+4
+
+15.2922756
+
+39.9141631
+
+0.8578431
+
+3.2078103
+
+0.3027245
+
+34.183673
+
+0.7843137
+
+0.2388060
+
+0.3272251
+
+70.1149425
+
+0.5432322
+
+0.2514142
+
    
+Mono/Mac/BAM
+
+426
+
+2.1775801
+
+68
+
+21
+
+23
+
+29
+
+48
+
+15
+
+44
+
+25
+
+32
+
+49
+
+49
+
+23
+
+3.5490605
+
+1.2875536
+
+1.4093137
+
+2.0223152
+
+4.8435923
+
+1.275510
+
+2.1568627
+
+1.4925373
+
+2.0942408
+
+2.8160920
+
+2.2181983
+
+1.4456317
+
    
+Ifn Responsive
+
+281
+
+1.4363850
+
+21
+
+14
+
+23
+
+22
+
+10
+
+16
+
+34
+
+30
+
+22
+
+26
+
+45
+
+18
+
+1.0960334
+
+0.8583691
+
+1.4093137
+
+1.5341702
+
+1.0090817
+
+1.360544
+
+1.6666667
+
+1.7910448
+
+1.4397906
+
+1.4942529
+
+2.0371209
+
+1.1313639
+
    
+Ccl4+
+
+166
+
+0.8485406
+
+11
+
+15
+
+18
+
+14
+
+13
+
+13
+
+13
+
+6
+
+23
+
+14
+
+13
+
+13
+
+0.5741127
+
+0.9196812
+
+1.1029412
+
+0.9762901
+
+1.3118063
+
+1.105442
+
+0.6372549
+
+0.3582090
+
+1.5052356
+
+0.8045977
+
+0.5885016
+
+0.8170962
+
    
+Proliferative
+
+27
+
+0.1380156
+
+5
+
+0
+
+2
+
+0
+
+5
+
+2
+
+2
+
+1
+
+5
+
+2
+
+3
+
+0
+
+0.2609603
+
+0.0000000
+
+0.1225490
+
+0.0000000
+
+0.5045409
+
+0.170068
+
+0.0980392
+
+0.0597015
+
+0.3272251
+
+0.1149425
+
+0.1358081
+
+0.0000000
+
    
+Total
+
+19563
+
+100.0000000
+
+1916
+
+1631
+
+1632
+
+1434
+
+991
+
+1176
+
+2040
+
+1675
+
+1528
+
+1740
+
+2209
+
+1591
+
+100.0000000
+
+100.0000000
+
+100.0000000
+
+100.0000000
+
+100.0000000
+
+100.000000
+
+100.0000000
+
+100.0000000
+
+100.0000000
+
+100.0000000
+
+100.0000000
+
+100.0000000
+
    
+
    Now we can use the function Random_Cells_Downsample to
+return a downsampled selection of cells from each identity. We can
+either set the num_cells parameter manually to the smallest
+group or simply provide "min".
    
+
    In this case that would 27 cells per group. which is a bit small to
+get representative sample when other groups are much larger. So
+alternatively, we can set a larger value (150 cells) and change the
+optional parameter allow_lower to TRUE. This
+means that all groups larger than 150 cells will get downsampled but any
+smaller will simply return all cells in that ident.
    
+
    +# random cells can either be return to environment
+random_cells_150 <- Random_Cells_Downsample(seurat_object = marsh_mouse_micro, num_cells = 150,
+    allow_lower = T)
+
+DoHeatmap(object = marsh_mouse_micro, features = micro_markers, cells = random_cells_150)
+
+# Or called within the `DoHeatmap` function.
+DoHeatmap(object = marsh_mouse_micro, features = micro_markers, cells = Random_Cells_Downsample(seurat_object = marsh_mouse_micro,
+    num_cells = 150, allow_lower = T))
    
+
    +DoHeatmap(object = marsh_mouse_micro, features = micro_markers, cells = Random_Cells_Downsample(seurat_object = marsh_mouse_micro,
+    num_cells = 150, allow_lower = T))
    
+
    
+*Much easier now to see expression across all clusters.*
    
+Much easier now to see expression across all clusters.
+
    
 
    
 
    
 
    
@@ -889,11 +1665,11 @@ 
    New default color palettes
 
    To best demonstrate rationale for this I’m going to use
 over-clustered version of the marsh_mouse_micro object.
    
-
    +
     DimPlot(object = marsh_mouse_over)
 DimPlot_scCustom(seurat_object = marsh_mouse_over)
    
 
    
-*`DimPlot_scCustom` also sets `label = TRUE` if `group.by = NULL` by default.*
    
+*`DimPlot_scCustom` also sets `label = TRUE` if `group.by = NULL` by default.*
    
 DimPlot_scCustom also sets label = TRUE if
 group.by = NULL by default.
 
    
@@ -909,11 +1685,11 @@ 
    Shuffle Points
 
    Here is example when plotting by donor in the human dataset to
 determine how well the dataset integration worked.
    
-
    +
     DimPlot(object = marsh_human_pm, group.by = "sample_id")
 DimPlot_scCustom(seurat_object = marsh_human_pm, group.by = "sample_id")
    
 
    
-***A.** Cannot tell how well integrated the samples are due to plotting one on top of the other.  **B.** Default plot using scCustomize `DimPlot_scCustom`.*
    
+***A.** Cannot tell how well integrated the samples are due to plotting one on top of the other.  **B.** Default plot using scCustomize `DimPlot_scCustom`.*
    
 A. Cannot tell how well integrated the samples are
 due to plotting one on top of the other. B. Default
 plot using scCustomize DimPlot_scCustom.
@@ -926,11 +1702,11 @@ 
    Split DimPlotsWhen plotting a split plot Seurat::DimPlot() simplifies
 the axes by implementing shared axes depending on the number of columns
 specified.
    
-
    +
     DimPlot(object = pbmc, split.by = "treatment")
 DimPlot(object = pbmc, split.by = "sample_id", ncol = 4)
    
 
    
-***A.** The default Seurat split.by looks ok when plots are all present on single row.  **B.** However, the visualization isn't so good when you starting wrapping plots into multiple rows.*
    
+***A.** The default Seurat split.by looks ok when plots are all present on single row.  **B.** However, the visualization isn't so good when you starting wrapping plots into multiple rows.*
    
 A. The default Seurat split.by looks ok when plots
 are all present on single row. B. However, the
 visualization isn’t so good when you starting wrapping plots into
@@ -940,10 +1716,10 @@ 
    Split DimPlotsBy default when using split.by with
 DimPlot_scCustom the layout is returned with an axes for
 each plot to make visualization of large numbers of splits easier.
    
-
    +
     DimPlot_scCustom(seurat_object = pbmc, split.by = "treatment", num_columns = 4, repel = TRUE)
    
 
    
-*Simplified visualization without having to think about the number of variables that are being plotted.*
    
+*Simplified visualization without having to think about the number of variables that are being plotted.*
    
 Simplified visualization without having to think about the number of
 variables that are being plotted.
 
    
@@ -952,9 +1728,9 @@ 
    Split DimPlotsDimPlot_scCustom by supplying
 split_seurat = TRUE
    
-
    +
     DimPlot_scCustom(seurat_object = pbmc, split.by = "treatment", num_columns = 4, repel = TRUE, split_seurat = TRUE)
    
-
    
+
    
 
    
 
    
 
    Figure Plotting
@@ -963,9 +1739,9 @@ 
    Figure PlottingDimPlot_scCustom simply set
 figure_plot = TRUE.
    
-
    +
     DimPlot_scCustom(seurat_object = pbmc, figure_plot = TRUE)
    
-
    
+
    
 
    
 
    
 
    
@@ -982,14 +1758,14 @@ 
    Highlight Cluster(s)
    +
     Cluster_Highlight_Plot(seurat_object = marsh_mouse_over, cluster_name = "7", highlight_color = "navy",
     background_color = "lightgray")
 
 Cluster_Highlight_Plot(seurat_object = marsh_mouse_over, cluster_name = "8", highlight_color = "forestgreen",
     background_color = "lightgray")
    
 
    
-*`Cluster_Highlight_Plot` takes identity or vector of identities and plots them in front of remaining unselected cells.*
    
+*`Cluster_Highlight_Plot` takes identity or vector of identities and plots them in front of remaining unselected cells.*
    
 Cluster_Highlight_Plot takes identity or vector of
 identities and plots them in front of remaining unselected cells.
 
    
@@ -999,10 +1775,10 @@ 
    Highlight 2+ clusters in the same
 
    
 
    Cluster_Highlight_Plot() also supports the ability to
 plot multiple identities in the same plot.
    
-
    +
     Cluster_Highlight_Plot(seurat_object = marsh_mouse_over, cluster_name = c("7", "8"), highlight_color = c("navy",
     "forestgreen"))
    
-
    
+
    
 
    NOTE: If no value is provided to highlight_color
 then all clusters provided to cluster_name will be plotted
 using single default color (navy).
    
@@ -1017,10 +1793,10 @@ 
    Highlight Meta Data
    +
     Meta_Highlight_Plot(seurat_object = marsh_mouse_micro, meta_data_column = "Transcription_Method",
     meta_data_highlight = "ENZYMATIC_NONE", highlight_color = "firebrick", background_color = "lightgray")
    
-
    
+
    
 
    
 
    Highlight 2+ factor levels in the same plot
 
    
@@ -1028,11 +1804,11 @@ 
    Highlight 2+ factor levels i
 levels from the same meta data column in the same plot, similar to
 plotting multiple identities with
 Cluster_Highlight_Plot()
    
-
    +
     Meta_Highlight_Plot(seurat_object = marsh_mouse_micro, meta_data_column = "Transcription_Method",
     meta_data_highlight = c("ENZYMATIC_NONE", "DOUNCE_NONE"), highlight_color = c("firebrick", "dodgerblue"),
     background_color = "lightgray")
    
-
    
+
    
 
    
 
    
 
    
@@ -1045,16 +1821,16 @@ 
    Highlight Cellscells_highlight parameter must be a named list.
    
 
    Let’s say we want to highlight cells with expression of
 MS4A1 above certain threshold.
    
-
    +
     # Get cell names
-MS4A1 <- WhichCells(object = pbmc, expression = MS4A1 > 3)
+MS4A1 <- WhichCells(object = pbmc, expression = MS4A1 > 3)
 
 # Make into list
 cells <- list(MS4A1 = MS4A1)
 
 # Plot
 Cell_Highlight_Plot(seurat_object = pbmc, cells_highlight = cells)
    
-
    
+
    
 
    
 
    Highlight 2+ sets of cells in the same plot
 
    
@@ -1062,15 +1838,15 @@ 
    Highlight 2+ sets of cells i
 sets of cells in the same plot, similar to plotting multiple identities
 with
 Cluster_Highlight_Plot()/Meta_Highlight_Plot().
    
-
    +
     # Get cell names and make list
-MS4A1 <- WhichCells(object = pbmc, expression = MS4A1 > 3)
-GZMB <- WhichCells(object = pbmc, expression = GZMB > 3)
+MS4A1 <- WhichCells(object = pbmc, expression = MS4A1 > 3)
+GZMB <- WhichCells(object = pbmc, expression = GZMB > 3)
 
 cells <- list(MS4A1 = MS4A1, GZMB = GZMB)
 # Plot
 Cell_Highlight_Plot(seurat_object = pbmc, cells_highlight = cells)
    
-
    
+
    
 
    
 
    
 
    
@@ -1079,19 +1855,19 @@ 
    DimPlot Layout Plots
    +
     DimPlot_All_Samples(seurat_object = pbmc, meta_data_column = "sample_id", num_col = 3, pt.size = 0.5)
    
 
    
-*Visualize all samples in simple plot layout.*
    
+*Visualize all samples in simple plot layout.*
    
 Visualize all samples in simple plot layout.
 
    
 
    
 
    Can unique color each plot by providing a vector of colors instead of
 single value
    
-
    +
     DimPlot_All_Samples(seurat_object = marsh_mouse_micro, meta_data_column = "Transcription", num_col = 2,
     pt.size = 0.5, color = c("firebrick3", "dodgerblue3"))
    
-
    
+
    
 
    
 
    
 
    
@@ -1099,9 +1875,7 @@ 
    DimPlot Layout Plots
 
-        
-
    
+      
    
 
 
    
 
@@ -1114,16 +1888,16 @@ 
    DimPlot Layout Plots
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
    
 
-  
 
 
-  
+
+
 
   
 
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 General Helpers & Utilities • scCustomize
-
+
 
 
 
 
 
-
 
 
 
-    
+
 
     
    
       
    
 
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  • 
   
   
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    • 
 
 
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    General Helpers & Utilities
    
             
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 2024
    
       
       Source: vignettes/articles/Helpers_and_Utilities.Rmd
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    General Helper/Utility Functions    replace = TRUE)
 pbmc$batch <- sample(c("Batch1", "Batch2"), size = ncol(pbmc), replace = TRUE)
    
 
    
-
    Add Mitochondrial & Ribosomal Percentages
-
    
-
    As discussed in QC
-Plotting vignette one the first steps after creating object if often
-to calculate and add mitochondrial and ribosomal count percentages per
-cell/nucleus.
    
-
    
-
    
-Add_Mito_Ribo()
-
    
-
    scCustomize contains easy wrapper function to automatically add both
-Mitochondrial and Ribosomal percentages to meta.data slot. If you are
-using mouse, human, marmoset, zebrafish, rat, drosophila, or rhesus
-macaque data all you need to do is specify the species
-parameter.
    
-
    -# These defaults can be run just by providing accepted species name
-pbmc <- Add_Mito_Ribo(object = pbmc, species = "human")
    
-
    To view list of accepted values for default species names simply set
-list_species_names = TRUE.
    
-
    -Add_Mito_Ribo(list_species_names = TRUE)
    
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
    
-
-Mouse_Options
-
-Human_Options
-
-Marmoset_Options
-
-Zebrafish_Options
-
-Rat_Options
-
-Drosophila_Options
-
-Macaque_Options
-
    
-1
-
-Mouse
-
-Human
-
-Marmoset
-
-Zebrafish
-
-Rat
-
-Drosophila
-
-Macaque
-
    
-2
-
-mouse
-
-human
-
-marmoset
-
-zebrafish
-
-rat
-
-drosophila
-
-macaque
-
    
-3
-
-Ms
-
-Hu
-
-CJ
-
-DR
-
-RN
-
-DM
-
-Rhesus
-
    
-4
-
-ms
-
-hu
-
-Cj
-
-Dr
-
-Rn
-
-Dm
-
-macaca
-
    
-5
-
-Mm
-
-Hs
-
-cj
-
-dr
-
-rn
-
-dm
-
-mmulatta
-
    
-6
-
-mm
-
-hs
-
-NA
-
-NA
-
-NA
-
-NA
-
-NA
-
    
-
    
-
    Non-default species
-
    
-
    However custom prefixes can be used for
-non-human/mouse/marmoset/rat/zebrafish/drosophila/macaque species with
-different annotations. Simply specify species = other and
-supply feature lists or regex patterns for your species of interest.
-NOTE: If desired please submit issue on GitHub for additional
-default species. Please include regex pattern or list of genes for both
-mitochondrial and ribosomal genes and I will add additional built-in
-defaults to the function.
    
-
    -# Using gene name patterns
-pbmc <- Add_Mito_Ribo(object = pbmc, species = "other", mito_pattern = "regexp_pattern", ribo_pattern = "regexp_pattern")
-
-# Using feature name lists
-mito_gene_list <- c("gene1", "gene2", "etc")
-ribo_gene_list <- c("gene1", "gene2", "etc")
-pbmc <- Add_Mito_Ribo(object = pbmc, species = "other", mito_features = mito_gene_list, ribo_features = ribo_gene_list)
-
-# Using combination of gene lists and gene name patterns
-pbmc <- Add_Mito_Ribo(object = pbmc, species = "Human", mito_features = mito_gene_list, ribo_pattern = "regexp_pattern")
    
-
    
-
    
-
    
-
    Warning Messages
-
    
-
    The added benefit of Add_Mito_Ribo is that it will
-return informative warnings if no Mitochondrial or Ribosomal features
-are found using the current species, features, or pattern
-specification.
    
-
    -# For demonstration purposes we can set `species = mouse` for this object of human cells
-pbmc <- Add_Mito_Ribo(object = pbmc, species = "mouse")
    
-
    ## Error in `Add_Mito_Ribo()`:
-## ! No Mito or Ribo features found in object using patterns/feature list
-##   provided.
-## ℹ Please check pattern/feature list and/or gene names in object.
    
-
    -# Or if providing custom patterns/lists and features not found
-pbmc <- Add_Mito_Ribo(object = pbmc, species = "other", mito_pattern = "^MT-", ribo_pattern = "BAD_PATTERN")
    
-
    ## Warning: No Ribo features found in object using pattern/feature list provided.
-## ℹ No column will be added to meta.data.
    
-
    Add_Mito_Ribo will also return warnings if columns are
-already present in @meta.data slot and prompt you to
-provide override if you want to run the function.
    
-
    -pbmc <- Add_Mito_Ribo(object = pbmc, species = "human")
    
-
    ## Error in `Add_Mito_Ribo()`:
-## ! Columns with "percent_mito" and/or "percent_ribo" already present in
-##   meta.data slot.
-## ℹ *To run function and overwrite columns set parameter `overwrite = TRUE` or
-##   change respective `mito_name`, `ribo_name`, and/or `mito_ribo_name`*
    
-
    
-
    
-
    LIGER Objects: Add_Mito_Ribo()
-
    
-
    scCustomize Add_Mito_Ribo also works seemlessly with
-LIGER objects.
    
-
    -liger_obj <- Add_Mito_Ribo(object = liger_obj, species = "human")
    
-
    
-
    
-
    
-
    Add Cell Complexity/Novelty QC Metrics
-
    
-
    In addition to metrics like number of features and UMIs it can often
-be helpful to analyze the complexity of expression within a single cell.
-scCustomize provides functions to add two of these metrics to meta
-data.
    
-
    
-
    Cell Complexity (log10(nFeature) / log10(nCount))
-
    
-
    scCustomize contains easy shortcut function to add a measure of cell
-complexity/novelty that can sometimes be useful to filter low quality
-cells. The metric is calculated by calculating the result of
-log10(nFeature) / log10(nCount).
    
-
    -# These defaults can be run just by providing accepted species name
-pbmc <- Add_Cell_Complexity(object = pbmc)
    
-
    NOTE: The function also works seemlessly with LIGER
-objects.
    
-
    
-
    
-
    Add Top Percent Expression QC Metric
-
    
-
    Additionally, (or alternatively), scCustomize contains another metric
-of complexity which is the top percent expression. The user supplies an
-integer value for num_top_genes (default is 50) which
-species the number of genes and the function returns percentage of
-counts occupied by top XX genes in each cell.
    
-
    -# These defaults can be run just by providing accepted species name
-pbmc <- Add_Top_Gene_Pct_Seurat(seurat_object = pbmc, num_top_genes = 50)
    
-
    
-
    
-
    
 
    Add All Cell QC Metrics with Single Function
 
    
-
    To simplify the process of adding cell QC metrics scCustomize
+
    One the first steps after creating object if often to calculate and
+add a number of different QC metrics at the cell level.
    
+
    To simplify the process of adding cell-level QC metrics scCustomize
 contains a wrapper function which can be customized to add all or some
-of the available QC metrics. The default parameters of the function
+of the available QC metrics. The functions have built-in support for
+large number of default species and support for both gene symbols or
+Ensembl IDs.
    
+
    The default parameters of the function
 Add_Cell_QC_Metrics will add:
    
 
      
 
    • Mitochondrial and Ribosomal Percentages (default and custom
 species).
      • 
+
    • Hemoglobin Percentages (default and custom species).
      • 
 
    • Cell Complexity (log10(nFeature) / log10(nCount).
      • 
 
    • Top XX Gene Percentage.
      • 
 
    • Percentage of counts for IEG (human and mouse only).
      • 
 
    • OXPHOS, APOP, and DNA Repair pathways (supported species only).
      • 
 
    • Cell Cycle Scoring (Human only).
      • 
 
    
-
    +
     pbmc <- Add_Cell_QC_Metrics(seurat_object = pbmc, species = "human")
    
+
    
+
    More details on cell QC metrics and scCustomize functions.
+
    
+
    For more details on cell QC metrics and the functions available in
+scCustomize please see Object
+QC Vignette. For details on plotting functions associated with QC
+metrics see QC
+Plotting vignette.
    
+
    
 
    
 
    
 
    Meta Data
@@ -507,7 +223,7 @@ 
    Extract all meta data (cel
 
    
 
    Fetch_Meta() functions as simple getter function to
 obtain meta data from object and return data.frame.
    
-
    +
     meta_data <- Fetch_Meta(object = pbmc)
 
 head(meta_data, 10)
    
@@ -552,10 +268,10 @@ 
    Extract all meta data (cel
 Memory CD4 T
 
 
-sample3
+sample4
 
 
-Batch2
+Batch1
 
 
 
@@ -575,10 +291,10 @@ 
    Extract all meta data (cel
 B
 
 
-sample5
+sample3
 
 
-Batch2
+Batch1
 
 
 
@@ -598,10 +314,10 @@ 
    Extract all meta data (cel
 Memory CD4 T
 
 
-sample4
+sample6
 
 
-Batch2
+Batch1
 
 
 
@@ -644,7 +360,7 @@ 
    Extract all meta data (cel
 NK
 
 
-sample4
+sample3
 
 
 Batch1
@@ -667,7 +383,7 @@ 
    Extract all meta data (cel
 Memory CD4 T
 
 
-sample6
+sample5
 
 
 Batch2
@@ -690,7 +406,7 @@ 
    Extract all meta data (cel
 CD8 T
 
 
-sample3
+sample4
 
 
 Batch1
@@ -713,10 +429,10 @@ 
    Extract all meta data (cel
 CD8 T
 
 
-sample4
+sample2
 
 
-Batch2
+Batch1
 
 
 
@@ -736,10 +452,10 @@ 
    Extract all meta data (cel
 Naive CD4 T
 
 
-sample6
+sample4
 
 
-Batch2
+Batch1
 
 
 
@@ -759,7 +475,7 @@ 
    Extract all meta data (cel
 FCGR3A+ Mono
 
 
-sample3
+sample1
 
 
 Batch2
@@ -774,7 +490,7 @@ 
    Extract sample-level meta da
 
    While cell-level meta data is helpful in some situations often all
 that is required is sample-level meta data. This can easily be extracted
 and filtered using Extract_Sample_Meta().
    
-
    +
     sample_meta <- Extract_Sample_Meta(object = pbmc, sample_name = "sample_id")
    
 
@@ -819,13 +535,13 @@ 
    Extract sample-level meta da
 pbmc3k
 
 
    
@@ -836,13 +552,13 @@ 
    Extract sample-level meta da
 pbmc3k
 
 
    
@@ -859,7 +575,7 @@ 
    Extract sample-level meta da
 sample4
 
 
    
@@ -870,7 +586,7 @@ 
    Extract sample-level meta da
 pbmc3k
 
 
    
@@ -907,7 +623,7 @@ 
    Remove columns tha
 may want to remove other columns too. This can be achieved using either
 positive or negative selection using variables_include or
 variables_exclude parameters.
    
-
    +
     sample_meta <- Extract_Sample_Meta(object = pbmc, sample_name = "sample_id", variables_exclude = c("nFeature_RNA",
     "nCount_RNA", "seurat_annotations", "orig.ident"))
    
 
    
 
    
-NA
+CD8 T
 
 
 sample2
 
 
-Batch2
+Batch1
 
 
    
 
    
-Memory CD4 T
+B
 
 
 sample3
 
 
-Batch2
+Batch1
 
 
    
 
    
-Batch2
+Batch1
 
 
    
 
    
-B
+Memory CD4 T
 
 
 sample5
@@ -893,7 +609,7 @@ 
    Extract sample-level meta da
 sample6
 
    		
 
-Batch2
+Batch1
 
 
    
 
    
@@ -941,7 +657,7 @@ 
    Remove columns tha
 sample2
 
 
    
@@ -952,7 +668,7 @@ 
    Remove columns tha
 sample3
 
 
    
@@ -963,7 +679,7 @@ 
    Remove columns tha
 sample4
 
 
    
@@ -985,7 +701,7 @@ 
    Remove columns tha
 sample6
 
 
    
@@ -998,7 +714,7 @@ 
    Merge with sample-level
 can be valuable to get summary information for those variables. This can
 be achieved by merging outputs with Median_Stats
 function.
    
-
    +
     sample_meta <- Extract_Sample_Meta(object = pbmc, sample_name = "sample_id", variables_exclude = c("nFeature_RNA",
     "nCount_RNA", "seurat_annotations", "orig.ident"))
 
@@ -1034,10 +750,10 @@ 
    Merge with sample-level
 Batch2
 
 
    
@@ -1048,13 +764,13 @@ 
    Merge with sample-level
 sample2
 
 
    
@@ -1065,10 +781,10 @@ 
    Merge with sample-level
 sample3
 
 
    
@@ -1102,10 +818,10 @@ 
    Merge with sample-level
 Batch2
 
 
    
@@ -1116,13 +832,13 @@ 
    Merge with sample-level
 sample6
 
 
    
@@ -1136,7 +852,7 @@ 
    Merge with sample-level
 NA
 
 
    
-Batch2
+Batch1
 
 
    
 
    
-Batch2
+Batch1
 
 
    
 
    
-Batch2
+Batch1
 
 
    
 
    
-Batch2
+Batch1
 
 
    
 
    
-2237.0
+2186
 
 
-830.0
+822.0
 
 
    
 
    
-Batch2
+Batch1
 
 
-2223.0
+2228
 
 
-810.0
+808.0
 
 
    
 
    
-Batch2
+Batch1
 
 
-2197.0
+2262
 
 
 816.0
@@ -1082,13 +798,13 @@ 
    Merge with sample-level
 sample4
 
    		
 
-Batch2
+Batch1
 
 
-2234.5
+2216
 
 
-815.5
+825.5
 
 
    
 
    
-2110.0
+2119
 
 
-797.5
+800.0
 
 
    
 
    
-Batch2
+Batch1
 
 
-2168.0
+2197
 
 
-820.0
+822.0
 
 
    
 
    
-2196.0
+2196
 
 
 816.0
@@ -1165,7 +881,7 @@ 
    Add sample-level meta data to obje
 information in Seurat object and sample-level meta data.
 
 
    This is example command:
    
-
    +
     obj <- Add_Sample_Meta(seurat_object = obj, meta_data = sample_meta, join_by_seurat = "orig.ident",
     join_by_meta = "sample_id")
    
 
    
@@ -1182,13 +898,14 @@ 
    Add feature meta data
-
    # Using features.tsv.gz file
-obj <- Add_Alt_Feature_ID(seurat_object = obj,
-features_tsv = "sample01/outs/filtered_feature_bc_matrix/features.tsv.gz", assay = "RNA")
-
-# Using hdf5 file
-obj <- Add_Alt_Feature_ID(seurat_object = obj,
-hdf5_file = "sample01/outs/outs/filtered_feature_bc_matrix.h5"", assay = "RNA")
    
+
    +# Using features.tsv.gz file
+obj <- Add_Alt_Feature_ID(seurat_object = obj, features_tsv = "sample01/outs/filtered_feature_bc_matrix/features.tsv.gz",
+    assay = "RNA")
+
+# Using hdf5 file
+obj <- Add_Alt_Feature_ID(seurat_object = obj, hdf5_file = "sample01/outs/outs/filtered_feature_bc_matrix.h5",
+    assay = "RNA")
    
 
    NOTE: If using features.tsv.gz file the file from either
 filtered or raw outputs can be used as they are identical.
    
 
    NOTE: If using hdf5 file the file from either
@@ -1203,13 +920,13 @@ 
    Check for Features/GenesscCustomize also makes forward-facing a number of utilities that are
 used internally in functions but may also have utility on their own.
    
 
    
-
    
-Gene_Present() to check for features.
+
    
+Feature_Present() to check for features.
 
    
-
    Gene_Present is fairly basic function to check if
+
    Feature_Present is fairly basic function to check if
 feature exists in data. It can be used with Seurat or LIGER objects as
 well as generic data formats (Matrix, data.frame, tibble).
    
-
    In addition to some warning messages Gene_Present
+
    In addition to some warning messages Feature_Present
 returns a list with 3 entries when run:
    
 
      
 
    • found_features: features found in the data.
      
@@ -1220,31 +937,25 @@ 
      
 present in input gene list.
 
        
 
      • If bad_features > 0 then
-Gene_Present will convert
+Feature_Present will convert
 the gene listbad_features` to all upper case and to
 sentence case and check against all possible features to see if wrong
 case was provided.
        • 
 
      
 
      • 
 
    
-
    +
     # Example gene list with all examples (found genes, wrong case (lower) and misspelled (CD8A
 # forgetting to un-shift when typing 8))
 gene_input_list <- c("CD14", "CD3E", "Cd4", "CD*A")
 
-genes_present <- Gene_Present(data = pbmc, gene_list = gene_input_list)
    
-
    ## Warning: `Gene_Present()` was deprecated in scCustomize 2.1.0.
-## ℹ Please use `Feature_Present()` instead.
-## ℹ Please adjust code now to prepare for full deprecation.
-## This warning is displayed once every 8 hours.
-## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
-## generated.
    
+genes_present <- Feature_Present(data = pbmc, features = gene_input_list)
    
 
    ## Warning: The following features were omitted as they were not found:
 ## ℹ Cd4 and CD*A
    
 
    ## Warning: NOTE: However, the following features were found: CD4
 ## ℹ Please check intended case of features provided.
    
 
    Now let’s look at the output:
    
-
    +
     genes_present
    
 
    ## $found_features
 ## [1] "CD14" "CD3E"
@@ -1258,10 +969,11 @@ 
    
 
    
 
    Turn warnings/messages off.
 
    
-
    By default Gene_Present has 3 sets of warnings/messages
-it prints to console when it finds issues. If using the function
-yourself on its own or wrapped inside your own function and you prefer
-no messages each of these can be toggled using optional parameters.
    
+
    By default Feature_Present has 3 sets of
+warnings/messages it prints to console when it finds issues. If using
+the function yourself on its own or wrapped inside your own function and
+you prefer no messages each of these can be toggled using optional
+parameters.
    
 
    
+library(qs)
    
 
     # read object
 marsh_micro <- qread("assets/marsh_2020_micro.qs")
 
 # Convert to liger
-marsh_liger <- rliger::seuratToLiger(objects = marsh_micro, combined.seurat = TRUE, use.idents = T,
-    use.tsne = T, meta.var = "orig.ident", remove.missing = FALSE)
-
-# Add meta data to LIGER \@cell.data slot
-marsh_liger@cell.data$Transcription <- marsh_micro@meta.data$Transcription
-marsh_liger@cell.data$Method <- marsh_micro@meta.data$Method
-marsh_liger@cell.data$Batch <- marsh_micro@meta.data$Batch
-marsh_liger@cell.data$Transcription_Method <- marsh_micro@meta.data$Transcription_Method
    
+marsh_liger <- as.liger(object = marsh_micro, datasetVar = "orig.ident")
+
    
+
    LIGER object version
+
    
+
    The Welch lab has recently released a major update to rliger package
+(v2.0.0+) which has substantial changes to object structure and major
+performance improvements over prior versions. The majority of liger
+functions in scCustomize v2.1.0 have been updated to work with old and
+new liger objects. However, a number of newer functions will be
+exclusive to rliger 2.0.0+.
    
+
    This vignette will be using rliger 2.0.0.
    
+
    
 
    
 
    Dimensionality Reduction Plotting
 
    
@@ -193,26 +204,9 @@ 
    Dimensionality Reduction Plotting
     DimPlot_LIGER(liger_object = marsh_liger)
    
 
    
-
    As you can see we get plot that looks very similar to thought
-generated by DimPlot_scCustom() or
+
    As you can see we get plot that looks very similar to those generated
+by DimPlot_scCustom() or
 Seurat::DimPlot().
    
-
    
-
    /* IMPORTANT: AXES LABELS /*
-
    
-
    Unfortunately, the liger/rliger package does not properly store the
-name of the dimensionality reduction technique used and labels all plots
-with tSNE1/tSNE2 or dr1/dr2.
    
-
    DimPlot_LIGER() solves this by providing extra parameter
-in the function that can be used to set labels. The first time you use
-DimPlot_LIGER in R session it will print a one-time message
-alerting you to the fact that this parameter exists and is set to “UMAP”
-by default (as it seems to be most commonly used method currently).
    
-
    However, this analysis object used tSNE so let’s change that
-parameter.
    
-
    -DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE")
    
-
    
-
    
 
    
 
    Optional functionality/Parameters
 
    
@@ -223,31 +217,29 @@ 
    Optional functionality/Parameters
 
    Plot combination
 
    
-
    -DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE", combination = T)
    
-
    
+
    +DimPlot_LIGER(liger_object = marsh_liger, combination = T)
    
+
    
 
    User can specify different color palettes for each plot
    
-
    +
     clu_color <- ColorBlind_Pal()
 sample_color <- DiscretePalette_scCustomize(num_colors = 12, palette = "alphabet")
 
-DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE", combination = T, colors_use_cluster = clu_color,
-    colors_use_meta = sample_color)
    
-
    
+DimPlot_LIGER(liger_object = marsh_liger, combination = T, colors_use_cluster = clu_color, colors_use_meta = sample_color)
    
+
    
 
    
 
    
 
    Grouping and Splitting Plots
 
    
 
    DimPlot_LIGER supports grouping and splitting plots by
 meta data variables or cluster and will return patchwork layout
    
+
    +DimPlot_LIGER(liger_object = marsh_liger, group_by = "Transcription_Method", colors_use_meta = JCO_Four())
    
+
    
 
    -DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE", group_by = "Transcription_Method",
-    colors_use_meta = JCO_Four())
    
-
    
-
    -DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE", group_by = "Cluster", split_by = "Transcription_Method",
+DimPlot_LIGER(liger_object = marsh_liger, group_by = "Cluster", split_by = "Transcription_Method",
     label = FALSE)
    
-
    
+
    
 
    
 
    
 
    Cluster Label Modification
@@ -268,13 +260,12 @@ 
    Cluster Label Modification
 label_color change label text color.
 
-
    -DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE")
-DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE", label = FALSE)
-DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE", label_repel = TRUE)
-DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE", label_repel = TRUE, label_box = TRUE,
-    label_size = 3)
    
-
    
+
    +DimPlot_LIGER(liger_object = marsh_liger)
+DimPlot_LIGER(liger_object = marsh_liger, label = FALSE)
+DimPlot_LIGER(liger_object = marsh_liger, label_repel = TRUE)
+DimPlot_LIGER(liger_object = marsh_liger, label_repel = TRUE, label_box = TRUE, label_size = 3)
    
+
    
 
    
 
    
 
    Raster Points
@@ -283,10 +274,10 @@ 
    Raster Pointsscattermore
 package. Axes, labels, and legends will remain in vector
 form.
    
-
    -DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE", raster = FALSE, label = FALSE)
-DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE", raster = TRUE, label = FALSE)
    
-
    
+
    +DimPlot_LIGER(liger_object = marsh_liger, raster = FALSE, label = FALSE)
+DimPlot_LIGER(liger_object = marsh_liger, raster = TRUE, label = FALSE)
    
+
    
 
    
 
    
 
    Restore ggplot2 default color scheme
@@ -294,9 +285,9 @@ 
    Restore ggplot2 default color sche
 
    If you would like to restore ggplot2 default color scheme but
 maintain the rest of the aesthetics of DimPlot_LIGER simply
 set parameter ggplot_default_colors = TRUE.
    
-
    -DimPlot_LIGER(liger_object = marsh_liger, reduction_label = "tSNE", ggplot_default_colors = TRUE)
    
-
    
+
    +DimPlot_LIGER(liger_object = marsh_liger, ggplot_default_colors = TRUE)
    
+
    
 
    
 
 
    
@@ -308,7 +299,7 @@ 
    Customized plotFactors Functionali
 Top_Genes_Factor)
    
 
    scCustomize contains function plotFactors_scCustom()
 which expands the functionality and customizes the visualizes of LIGER’s
-plotFactors() function.
    
+plotFactors() function.
    
 
    
 
    Plots Created
 
    
@@ -316,12 +307,12 @@ 
    Plots Created
    +
-
    
+
    
 
    
 
    
 
    Additional Plot Save/Return Functionality
@@ -360,14 +351,7 @@ 
    Additional Factor Plot Functionali
 ggplot_default_colors parameter can be specified if you
 would like to return this plot to using the ggplot2/hue palette.
 
-
    
-
      
-
    • 
-reorder_datasets new order to plot datasets in. By
-default plots in factor level order from the @cell.data slot but this can be reordered just
-for plotting without changing the underlying object.
      • 
-
    
-
    
+
    
 
    
 
    
 
    Added Dimensionality Reduction Functionality
@@ -383,7 +367,7 @@ 
    Added Dimensionality Reduc
 cell hiding). Default is FALSE.
 
 
    
-
    /* IMPORTANT: AXES LABELS /*
+
    /* IMPORTANT: AXES LABELS /*
 
    
 
    Unfortunately, the liger/rliger package does not properly store the
 name of the dimensionality reduction technique used and labels all plots
@@ -406,59 +390,24 @@ 
    Extract Top Loading Genes per Fact
 the list of genes that loads highly on particular iNMF factor.
    NOTE: This function simply extracts top loading genes in order from
 given factor. It does not assess whether that number of genes is
 significant, etc.
    
-
    +
     top20_factor6 <- Top_Genes_Factor(liger_object = marsh_liger, liger_factor = 6, num_genes = 20)
 
 head(top20_factor6, 5)
    
-
    ## [1] "Ifit3"  "Ifit2"  "Ifit3b" "Ifit1"  "Irf7"
    
-
    
-
    
-
    Convert LIGER to Seurat
-
    
-
    The liger/rliger package already contains a function
-ligerToSeurat() to convert LIGER objects to Seurat Objects.
-However, during this transfer a few things have issues crop up:
    
-
      
-
    • All meta data except the “dataset” column from
-liger_object@cell.data is lost.
      • 
-
    • Seurat dimensionality reduction is set to tSNE regardless of method
-used in LIGER analysis
      • 
-
    • Seurat assay name not specified
      • 
-
    
-
    scCustomize contains modified version of this function which extends
-the Seurat function as.Seurat()
-that solves these issues with some extra parameters:
    
-
      
-
    • 
-keep_meta logical. Whether to keep meta data from the
-@cell.data slot in LIGER object. Default is TRUE.
      • 
-
    • 
-reduction_label Name of dimensionality reduction
-technique used (e.g., tSNE, UMAP, etc). Ensures dim names are set
-correctly in Seurat object.
      • 
-
    • 
-seurat_assay Name of assay to use for data in Seurat
-object. Default is “RNA”.
      • 
-
    • 
-assay_type Specify whether to create V3/4 vs V5 Seurat
-assays.
      • 
-
    
-
    -seurat_obj <- as.Seurat(x = liger_object, reduction_label = "UMAP")
    
+
    ## [1] "Junb" "Jun"  "Klf2" "Klf6" "Btg2"
    
 
    
 
    
-
    Add Mitochondrial & Ribosomal Percentages
+
    Add Cell QC Metrics
 
    
-
    For more information on adding mitochondrial and ribosomal count
-percentages to LIGER objects see General
-Utilities and Helpers Vignette for information on
-Add_Mito_Ribo.
    
+
    For more information on adding cell QC metricss to LIGER objects see
+Object
+QC Vignette for information.
    
 
    
 
    
 
    Variable Gene Selection
 
    
 
    By default when selecting highly variable genes in LIGER using
-rliger::selectGenes() LIGER performs gene selection across
+rliger::selectGenes() LIGER performs gene selection across
 all datasets in the object and then can either take the union or
 intersection of those lists (default is union). However, sometimes for
 analysis you may want to select highly variable genes from all data
@@ -471,7 +420,7 @@ 
    Variable Gene Selection
    
-
    +
     # Select highly variable genes based on threshold
 marsh_liger <- Variable_Features_ALL_LIGER(liger_object = marsh_liger, var.thresh = 0.3)
 
@@ -482,29 +431,27 @@ 
    Variable Gene SelectionGene Utilities
 
    
 
    As discussed in helpers
-vignette, the Gene_Present() function can be used to
+vignette, the Gene_Present() function can be used to
 check if list of genes are present in a LIGER object.
    
 
    By default this will query all datasets in the object to create
 unified gene list and check input gene list against that list.
    
-
    +
     gene_input_list <- c("P2ry12", "Fcrls", "Aif1")
 
-genes_present <- Gene_Present(data = marsh_liger, gene_list = gene_input_list)
    
+genes_present <- Feature_Present(data = marsh_liger, features = gene_input_list)
    
 
    However you can check individual datasets within object by supplying
 those matrices to the data parameter.
    
-
    +
     gene_input_list <- c("P2ry12", "Fcrls", "Aif1")
 
-genes_present <- Gene_Present(data = marsh_liger@raw.data[[1]], gene_list = gene_input_list)
    
+genes_present <- Feature_Present(data = marsh_liger@datasets[[1]], features = gene_input_list)
    
 
    
 
    
   
    
 
   
+      
    
 
 
    
 
@@ -517,16 +464,16 @@ 
    Gene Utilities
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
 
-  
 
 
-  
+
+
 
   
 
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diff --git a/docs/articles/Markers_and_Cluster_Annotation.html b/docs/articles/Markers_and_Cluster_Annotation.html
index 421a8a64f4..81ba2f75eb 100644
--- a/docs/articles/Markers_and_Cluster_Annotation.html
+++ b/docs/articles/Markers_and_Cluster_Annotation.html
@@ -6,20 +6,19 @@
 
 
 Marker Identification & Cluster Annotation Helpers • scCustomize
-
+
 
 
 
 
 
-
 
 
 
-    
+
 
     
    
       
    
 
@@ -48,7 +47,7 @@
 
  • 
   
   
@@ -128,7 +133,7 @@
 
    • 
 
 
-      
+
 
       
 
    
@@ -137,7 +142,7 @@
       
    Marker Identification & Cluster Annotation
 Helpers
    
             
-            
    Compiled: February 28,
+            
    Compiled: December 05,
 2024
    
       
       Source: vignettes/articles/Markers_and_Cluster_Annotation.Rmd
@@ -166,7 +171,7 @@ 
    Marker Identification & Cl
 library(magrittr)
 library(Seurat)
 library(scCustomize)
-library(qs)
+library(qs)
 
 # Load example dataset for tutorial
 pbmc <- pbmc3k.SeuratData::pbmc3k.final
    
@@ -1131,9 +1136,7 @@ 
    Renaming Clusters
 
-        
-
+      
 
 
 
@@ -1146,16 +1149,16 @@ 
    Renaming Clusters
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.0.
    
 
 
       
 
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/articles/Misc_Functions.html b/docs/articles/Misc_Functions.html
index e0d7db210e..39891c0bb0 100644
--- a/docs/articles/Misc_Functions.html
+++ b/docs/articles/Misc_Functions.html
@@ -6,20 +6,19 @@
 
 
 Misc Functions • scCustomize
-
+
 
 
 
 
 
-
 
 
 
-    
+
 
     
    
       
    
 
@@ -48,7 +47,7 @@
 
  • 
   
   
@@ -128,14 +133,14 @@
 
    • 
 
 
-      
+
 
       
    
   
    
     
    
       
    Misc Functions
    
             
-            
    Compiled: February 28,
+            
    Compiled: December 05,
 2024
    
       
       Source: vignettes/articles/Misc_Functions.Rmd
@@ -232,9 +237,7 @@ 
    Adapting Function Yourself
 
-        
-
    
+      
    
 
 
    
 
@@ -247,16 +250,16 @@ 
    Adapting Function Yourself
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.0.
    
 
 
       
 
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/articles/Object_Conversion.html b/docs/articles/Object_Conversion.html
index af59481e56..4a5428a7d5 100644
--- a/docs/articles/Object_Conversion.html
+++ b/docs/articles/Object_Conversion.html
@@ -6,20 +6,19 @@
 
 
 Object Format Conversion • scCustomize
-
+
 
 
 
 
 
-
 
 
 
-    
+
 
     
    
       
    
 
@@ -48,7 +47,7 @@
 
  • 
   
   
@@ -128,7 +133,7 @@
 
    • 
 
 
-      
+
 
       
 
    
@@ -136,7 +141,7 @@
     
    
       
    Object Format Conversion
    
             
-            
    Compiled: February 28,
+            
    Compiled: December 05,
 2024
    
       
       Source: vignettes/articles/Object_Conversion.Rmd
@@ -165,108 +170,22 @@ 
    Converting between scRNA-s
 
+library(qs)
    
 
    Load Seurat Object & Add QC Data
    
 
     # read object
 pbmc <- pbmc3k.SeuratData::pbmc3k.final
-pbmc <- UpdateSeuratObject(pbmc)
+pbmc <- UpdateSeuratObject(pbmc)
 
-pbmc <- Add_Cell_QC_Metrics(seurat_object = pbmc, species = "human")
    
+pbmc <- Add_Cell_QC_Metrics(object = pbmc, species = "human")
    
 
    We’ll also add some random meta data variables to pbmc data form use
 in this vignette
    
 
     pbmc$sample_id <- sample(c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6"), size = ncol(pbmc),
     replace = TRUE)
    
 
    
-
    Convert Seurat Objects to LIGER Objects
-
    
-
    scCustomize contains the conversion function as.LIGER().
-This function has a few advantages over the conversion function
-rliger::seuratToLiger().
    
-
      
-
    • 
-as.liger will keep all meta data and transfer
-it to LIGER by default.
      
-
      • 
-
    • If a dimensionality reduction is transferred as.liger
-will also store a reduction key for use with scCustomize LIGER plotting
-functions to correctly set plot axes.
      
-
      • 
-
    • If converting a list of Seurat objects and keeping Seurat variable
-genes then as.liger can either take union or intersection
-of genes between objects.
      
-
      • 
-
    • 
-as.liger has additional internal checks to ensure
-compatibility with both Seurat V3/4 & V5 object structures.
      • 
-
    
-
    -pbmc_liger <- as.LIGER(x = pbmc, group.by = "sample_id")
    
-
    ## • Checking Seurat object validity
-## • Creating LIGER object.
-## • Normalizing data.
    
-
    -pbmc_liger
    
-
    ## An object of class liger 
-## with 6 datasets and
-##  2638 total cells.
    
-
    Confirm that information from meta.data slot was transferred to LIGER
-object.
    
-
    -head(colnames(x = pbmc_liger@cell.data), 10)
    
-
    ##  [1] "nUMI"               "nGene"              "dataset"           
-##  [4] "orig.ident"         "seurat_annotations" "percent.mt"        
-##  [7] "RNA_snn_res.0.5"    "seurat_clusters"    "percent_mito"      
-## [10] "percent_ribo"
    
-
    
-
    
-
    Convert LIGER objects to Seurat Objects
-
    
-
    The liger/rliger package already contains a function
-rliger::seuratToLiger() to convert LIGER objects to Seurat
-Objects. However, during this transfer a few things have issues crop
-up:
    
-
      
-
    • All meta data except the “dataset” column from
-liger_object@cell.data is lost.
      • 
-
    • Seurat dimensionality reduction is set to tSNE regardless of method
-used in LIGER analysis
      • 
-
    • Seurat assay name not specified
      • 
-
    
-
    As of scCustomize v2.1.0 converting to Seurat objects from Liger can
-be accomplished using as.liger function which functions
-identically to previous function Liger_to_Seurat().
-Liger_to_Seurat() will continue to work until v2.2.0 at
-which point it will be completely deprecated.
    
-
    scCustomize contains modified version of this function which extends
-the Seurat function as.Seurat()
-that solves these issues with some extra parameters:
    
-
      
-
    • 
-keep_meta logical. Whether to keep meta data from the
-@cell.data slot in LIGER object. Default is TRUE.
      • 
-
    • 
-reduction_label Name of dimensionality reduction
-technique used (e.g., tSNE, UMAP, etc). Ensures dim names are set
-correctly in Seurat object.
      • 
-
    • 
-seurat_assay Name of assay to use for data in Seurat
-object. Default is “RNA”.
      
-
      • 
-
    • 
-assay_type Specify whether to create V3/4 vs V5 Seurat
-assays.
      • 
-
    
-
    -new_seurat <- as.Seurat(x = pbmc_liger, reduction_label = "UMAP")
    
-
    ## Preparing & merging matrices.
-## Creating final sparse matrix.
-## Normalizing layer: counts
    
-
    
-
    
 
    Convert Seurat or LIGER objects to Anndata objects
 
    
 
    scCustomize also allows for the conversion of Seurat or LIGER objects
@@ -293,19 +212,20 @@ 
    Convert Seurat or LI
 
 
 
-
    +
     as.anndata(x = pbmc, file_path = "~/Desktop", file_name = "pbmc_anndata.h5ad")
    
-
    ## • Checking Seurat object validity & Extracting Data
+
    ## • Checking Seurat object validity
+## • Extracting Data from RNA assay to transfer to anndata.
 ## The following columns were removed as they contain identical values for all
 ## rows:
 ## ℹ orig.ident
 ## • Creating anndata object.
 ## • Writing anndata file: "/Users/marsh_mbp/Desktop/pbmc_anndata.h5ad"
    
 
    ## AnnData object with n_obs × n_vars = 2638 × 13714
-##     obs: 'nCount_RNA', 'nFeature_RNA', 'seurat_annotations', 'percent.mt', 'RNA_snn_res.0.5', 'seurat_clusters', 'percent_mito', 'percent_ribo', 'percent_mito_ribo', 'log10GenesPerUMI', 'percent_top50', 'percent_oxphos', 'percent_apop', 'percent_dna_repair', 'percent_ieg', 'S.Score', 'G2M.Score', 'Phase', 'sample_id'
-##     var: 'vst.mean', 'vst.variance', 'vst.variance.expected', 'vst.variance.standardized', 'vst.variable'
+##     obs: 'nCount_RNA', 'nFeature_RNA', 'seurat_annotations', 'percent.mt', 'RNA_snn_res.0.5', 'seurat_clusters', 'percent_mito', 'percent_ribo', 'percent_mito_ribo', 'log10GenesPerUMI', 'percent_top50', 'percent_oxphos', 'percent_apop', 'percent_dna_repair', 'percent_ieg', 'percent_hemo', 'S.Score', 'G2M.Score', 'Phase', 'sample_id'
+##     var: 'names'
 ##     obsm: 'X_pca', 'X_umap'
-##     layers: 'counts'
    
+##     layers: 'counts_RNA'
    
 
    
 
    
 
    Convert Seurat assay type within an object
@@ -321,7 +241,7 @@ 
    Convert Seurat assay type wi
 
    
 
    Convert V3/4 to V5
 
    
-
    +
     # Convert to V5/Assay5 structure
 pbmc_V5 <- Convert_Assay(seurat_object = pbmc, convert_to = "V5")
 
@@ -335,7 +255,7 @@ 
    Convert V3/4 to V5
 
    Convert V5 > V3/4
 
    
-
    +
     # Convert to V3/4/Assay structure
 pbmc_V3 <- Convert_Assay(seurat_object = pbmc_V5, convert_to = "V3")
 
@@ -400,9 +320,7 @@ 
    Accepted values for convert_to
 
-        
-
    
+      
    
 
 
    
 
@@ -415,16 +333,16 @@ 
    Accepted values for convert_to
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/articles/Object_QC_Functions.html b/docs/articles/Object_QC_Functions.html
new file mode 100644
index 0000000000..d9ac14efdb
--- /dev/null
+++ b/docs/articles/Object_QC_Functions.html
@@ -0,0 +1,671 @@
+
+
+
+
+
+
+
+Object QC Functions • scCustomize
+
+
+
+
+
+
+
+
+
+
+
+    
    
+      
    
+
+
+
+
+      
    
+
    
+  
    
+    
    
+      
    Object QC Functions
    
+            
+            
    Compiled: December 05,
+2024
    
+      
+      Source: vignettes/articles/Object_QC_Functions.Rmd
+      
+
+    
    
+
+    
+    
+
    
+
+
    
+
    Quality control of scRNA-seq objects
+
    
+
    scCustomize has several helper functions to simplify/streamline what
+is nearly always the first and most critical choices when starting an
+analysis: performing quality control and filtering.
    
+
    Let’s load packages and raw data object for this tutorial.
    
+
    +# Load Packages
+library(ggplot2)
+library(dplyr)
+library(magrittr)
+library(patchwork)
+library(Seurat)
+library(scCustomize)
+
+pbmc <- pbmc3k.SeuratData::pbmc3k
    
+
    We’ll add some random meta data variables to pbmc data form use in
+this vignette
    
+
    +pbmc$sample_id <- sample(c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6"), size = ncol(pbmc),
+    replace = TRUE)
+pbmc$batch <- sample(c("Batch1", "Batch2"), size = ncol(pbmc), replace = TRUE)
    
+
    
+
    Cross-compatibility of QC Functions
+
    
+
    
+
    Support for Seurat and LIGER Objects
+
    
+
    All of scCustomize’s functions to add quality control metrics are
+100% cross compatible across Seurat and LIGER objects using the same
+function calls. For more details on QC specific plotting functions see
+QC
+Plotting & Analysis Vignette.
    
+
    
+
    
+
    Support for gene symbols and Ensembl IDs
+
    
+
    Additionally, all of the QC functions support objects that use either
+gene symbols or Ensembl IDs. Ensembl IDs for default species (see below)
+are from Ensembl version 112 (updated in scCustomize on 4/29/2024).
    
+
    If your object using ensembl IDs as features names then simply add
+ensembl_ids parameter that is present in all QC
+functions.
    
+
    +# Using gene name patterns
+obj <- Add_Mito_Ribo(object = obj, species = "Human", ensembl_ids = TRUE)
    
+
    
+
    
+
    
+
    Default Species Support
+
    
+
    Many of the QC functions commonly performed depend on genes within a
+particular family that have similar naming patterns (e.g., Mitochondrial
+genes) or are species specific (see msigdb dependent parts of
+Add_Cell_QC_Metrics()).
    
+
    To simplify the process of needing to remember species-specific
+patterns (or find Ensembl ID gene lists)
    
+
    If you are using mouse, human, marmoset, zebrafish, rat, drosophila,
+rhesus macaque, or chicken data all you need to do is specify the
+species parameter in the functions described below using
+one of the following accepted names.
    
+
+
+
+
+
+
+
+
+
+
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+
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+
    
+
+Mouse_Options
+
+Human_Options
+
+Marmoset_Options
+
+Zebrafish_Options
+
+Rat_Options
+
+Drosophila_Options
+
+Macaque_Options
+
+Chicken_Options
+
    
+1
+
+Mouse
+
+Human
+
+Marmoset
+
+Zebrafish
+
+Rat
+
+Drosophila
+
+Macaque
+
+Chicken
+
    
+2
+
+mouse
+
+human
+
+marmoset
+
+zebrafish
+
+rat
+
+drosophila
+
+macaque
+
+chicken
+
    
+3
+
+Ms
+
+Hu
+
+CJ
+
+DR
+
+RN
+
+DM
+
+Rhesus
+
+Gallus
+
    
+4
+
+ms
+
+hu
+
+Cj
+
+Dr
+
+Rn
+
+Dm
+
+macaca
+
+gallus
+
    
+5
+
+Mm
+
+Hs
+
+cj
+
+dr
+
+rn
+
+dm
+
+mmulatta
+
+Gg
+
    
+6
+
+mm
+
+hs
+
+NA
+
+NA
+
+NA
+
+NA
+
+NA
+
+gg
+
    
+
    
+
    Non-default species
+
    
+
    However custom prefixes can be used for species with different
+annotations. Simply specify species = other and supply
+feature lists or regex patterns for your species of interest. NOTE:
+If desired please submit issue on GitHub for additional default species.
+Please include regex pattern or list of genes for both mitochondrial and
+ribosomal genes and I will add additional built-in defaults to the
+function.
    
+
    What is example of how this works?
+
    +# Using gene name patterns
+pbmc <- Add_Mito_Ribo(object = pbmc, species = "other", mito_pattern = "regexp_pattern_mito", ribo_pattern = "regexp_pattern_ribo")
+
+# Using feature name lists
+mito_gene_list <- c("gene1", "gene2", "etc")
+ribo_gene_list <- c("gene1", "gene2", "etc")
+pbmc <- Add_Mito_Ribo(object = pbmc, species = "other", mito_features = mito_gene_list, ribo_features = ribo_gene_list)
+
+# Using combination of gene lists and gene name patterns
+pbmc <- Add_Mito_Ribo(object = pbmc, species = "Human", mito_features = mito_gene_list, ribo_pattern = "regexp_pattern_ribo")
    
+
     
    
+
    
+
    
+
    
+
    Add All Cell QC Metrics with Single Function
+
    
+
    To simplify the process of adding cell QC metrics scCustomize
+contains a wrapper function which can be customized to add all or some
+of the available QC metrics. This vignette will describe each of these
+in more detail below but using the default parameters of the function
+Add_Cell_QC_Metrics() will add:
    
+
      
+
    • Mitochondrial and Ribosomal Percentages (default and custom
+species).
      • 
+
    • Hemoglobin percentages (default and custom species).
      
+
      • 
+
    • Cell Complexity (log10(nFeature) / log10(nCount).
      • 
+
    • Top XX Gene Percentage.
      • 
+
    • Percentage of counts for IEG (human and mouse only).
      • 
+
    • OXPHOS, APOP, and DNA Repair pathways (supported species only).
      • 
+
    • Cell Cycle Scoring (Human only).
      • 
+
    
+
    +pbmc <- Add_Cell_QC_Metrics(object = pbmc, species = "human")
    
+
    ## • Adding Mito/Ribo Percentages to meta.data.
+## Adding Percent Mitochondrial genes for human using gene symbol pattern: "^MT-".
+## Adding Percent Ribosomal genes for human using gene symbol pattern: "^RP[SL]".
+## Adding Percent Mito+Ribo by adding Mito & Ribo percentages.
+## • Adding Cell Complexity #1 (log10GenesPerUMI) to meta.data.
+## • Adding Cell Complexity #2 (Top 50 Percentages) to meta.data.
+## Calculating percent expressing top 50 for layer: counts
+## • Adding MSigDB Oxidative Phosphorylation, Apoptosis, and DNA Repair
+##   Percentages to meta.data.
+## • Adding IEG Percentages to meta.data.
+## • Adding Hemoglobin Percentages to meta.data.
+## Adding Percent Hemoglobin for Human using gene symbol pattern: "^HB[^(P)]".
+## • Adding Cell Cycle Scoring to meta.data.
+## Calculating Cell Cycle Scores.
    
+
    
+
    
+
    Add QC Metrics Individually
+
    
+
    If you only want to add some but not all metrics you can either
+customize Add_Cell_QC_Metrics or use the individual
+functions.
    
+
    
+
    Add Mitochondrial & Ribosomal Percentages
+
    
+
    If you just want to calculate and add mitochondrial and ribosomal
+count percentages per cell/nucleus you can use
+Add_Mito_Ribo.
    
+
    
+
    
+Add_Mito_Ribo()
+
    
+
    scCustomize contains easy wrapper function to automatically add both
+Mitochondrial and Ribosomal percentages to meta.data slot. If you are
+using mouse, human, marmoset, zebrafish, rat, drosophila, rhesus
+macaque, or chicken data all you need to do is specify the
+species parameter.
    
+
    +# These defaults can be run just by providing accepted species name
+pbmc <- Add_Mito_Ribo(object = pbmc, species = "human")
    
+
    
+
    
+
    Analysis with two species
+
    
+
    Some analyses are performed with cells aligned to a genome that
+contains multiple species (see Cell Ranger/10X documentation for more
+info). scCustomize now supports adding mitochondrial and ribosomal
+percentages for these datasets using optional parameters. Here we will
+use example data provided by 10X Genomics here.
    
+
    +pbmc_dual_species <- Read10X_h5(filename = "~/Downloads/10k_hgmm_3p_gemx_Multiplex_count_raw_feature_bc_matrix.h5")
+
+pbmc_dual_species <- CreateSeuratObject(counts = pbmc_dual_species, min.cells = 5, min.features = 500)
    
+
    For dual species analyses the only other information you need to
+provide is what the prefixes are used in front of gene IDs. In this case
+the prefixes are “GRCh38-” and “GRCm39-”.
    
+
    +pbmc_dual_species <- Add_Mito_Ribo(object = pbmc_dual_species, species = c("human", "mouse"), species_prefix = c("GRCh38-",
+    "GRCm39-"))
    
+
    
+
    
+
    Warning Messages
+
    
+
    The added benefit of Add_Mito_Ribo is that it will
+return informative warnings if no Mitochondrial or Ribosomal features
+are found using the current species, features, or pattern
+specification.
    
+
    +# For demonstration purposes we can set `species = mouse` for this object of human cells
+pbmc <- Add_Mito_Ribo(object = pbmc, species = "mouse")
    
+
    ## Error in `Add_Mito_Ribo()`:
+## ! Columns with "percent_mito" and/or "percent_ribo" already present in
+##   meta.data slot.
+## ℹ *To run function and overwrite columns set parameter `overwrite = TRUE` or
+##   change respective `mito_name`, `ribo_name`, and/or `mito_ribo_name`*
    
+
    +# Or if providing custom patterns/lists and features not found
+pbmc <- Add_Mito_Ribo(object = pbmc, species = "other", mito_pattern = "^MT-", ribo_pattern = "BAD_PATTERN")
    
+
    ## Warning: No Ribo features found in object using pattern/feature list provided.
+## ℹ No column will be added to meta.data.
    
+
    ## Adding Percent Mitochondrial genes for other using gene symbol
+## pattern: "^MT-".
    
+
    Add_Mito_Ribo will also return warnings if columns are
+already present in @meta.data slot and prompt you to
+provide override if you want to run the function.
    
+
    +pbmc <- Add_Mito_Ribo(object = pbmc, species = "human")
    
+
    ## Error in `Add_Mito_Ribo()`:
+## ! Columns with "percent_mito" and/or "percent_ribo" already present in
+##   meta.data slot.
+## ℹ *To run function and overwrite columns set parameter `overwrite = TRUE` or
+##   change respective `mito_name`, `ribo_name`, and/or `mito_ribo_name`*
    
+
    
+
    
+
    
+
    
+
    Add Cell Complexity/Novelty QC Metrics
+
    
+
    In addition to metrics like number of features and UMIs it can often
+be helpful to analyze the complexity of expression within a single cell.
+scCustomize provides functions to add two of these metrics to meta
+data.
    
+
    
+
    Cell Complexity (log10(nFeature) / log10(nCount))
+
    
+
    scCustomize contains easy shortcut function to add a measure of cell
+complexity/novelty that can sometimes be useful to filter low quality
+cells. The metric is calculated by calculating the result of
+log10(nFeature) / log10(nCount).
    
+
    +# These defaults can be run just by providing accepted species name
+pbmc <- Add_Cell_Complexity(object = pbmc)
    
+
    
+
    
+
    Add Top Percent Expression QC Metric
+
    
+
    Additionally, (or alternatively), scCustomize contains another metric
+of complexity which is the top percent expression. The user supplies an
+integer value for num_top_genes (default is 50) which
+species the number of genes and the function returns percentage of
+counts occupied by top XX genes in each cell.
    
+
    +# These defaults can be run just by providing accepted species name
+pbmc <- Add_Top_Gene_Pct(object = pbmc, num_top_genes = 50)
    
+
    
+
    
+
    
+
    Add Hemoglobin Percentage
+
    
+
    scCustomize also contains function to add percentage of counts for
+hemoglobin genes. Use of this metric is much more situational. If your
+experiment has the potential for red blood cell contamination but you
+want to avoid that then this can be helpful. A high percentage of
+hemoglobin counts may indicate that your sample has high amount of
+ambient RNA present or RBCs in the cells captured.
    
+
    +pbmc <- Add_Hemo(object = pbmc, species = "human")
    
+
    
+
    
+
    Add QC Metrics from Pathway Gene Lists
+
    
+
    In addition to those standard QC metrics it can be helpful when using
+networ- based QC analysis to add the percent of expression of genes
+related to common pathways. This function and the network-based analysis
+is further extension of the analysis/QC from our recent publication:
+Gazestani & Kamath et al., 2023 (Cell).
    
+
    In scCustomize the percent of gene expression from the following gene
+lists can be added as part of the Add_Cell_QC_Metrics:
    
+
      
+
    • Immediate Early Genes (for human and mouse only)
+
        
+
      • Can be used in part to examine potential impact of dissociation or
+post-mortem signatures (Marsh et al.,
+2022) or to identify acutely perturbed populations (gene list
+from Wu et
+al., 2017)
        • 
+
      
+
      • 
+
    • Oxidative Phosphorylation, Apoptosis, & DNA Repair (all default
+species except Marmoset)
+
+
      • 
+
    
+
    
+
    
+  
    
+
+  
+
+
    
+
+
+
+      
    
+  
    
+
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    
+
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
    
+
+
+
+
+
+
+  
+
diff --git a/docs/articles/Object_QC_Functions_files/kePrint-0.0.1/kePrint.js b/docs/articles/Object_QC_Functions_files/kePrint-0.0.1/kePrint.js
new file mode 100644
index 0000000000..e6fbbfc44d
--- /dev/null
+++ b/docs/articles/Object_QC_Functions_files/kePrint-0.0.1/kePrint.js
@@ -0,0 +1,8 @@
+$(document).ready(function(){
+    if (typeof $('[data-toggle="tooltip"]').tooltip === 'function') {
+        $('[data-toggle="tooltip"]').tooltip();
+    }
+    if ($('[data-toggle="popover"]').popover === 'function') {
+        $('[data-toggle="popover"]').popover();
+    }
+});
diff --git a/docs/articles/Object_QC_Functions_files/lightable-0.0.1/lightable.css b/docs/articles/Object_QC_Functions_files/lightable-0.0.1/lightable.css
new file mode 100644
index 0000000000..3be3be9046
--- /dev/null
+++ b/docs/articles/Object_QC_Functions_files/lightable-0.0.1/lightable.css
@@ -0,0 +1,272 @@
+/*!
+ * lightable v0.0.1
+ * Copyright 2020 Hao Zhu
+ * Licensed under MIT (https://github.com/haozhu233/kableExtra/blob/master/LICENSE)
+ */
+
+.lightable-minimal {
+  border-collapse: separate;
+  border-spacing: 16px 1px;
+  width: 100%;
+  margin-bottom: 10px;
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+
+.lightable-minimal td {
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+.lightable-minimal thead tr:last-child th {
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+
+.lightable-minimal tbody tr:first-child td {
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+.lightable-minimal.lightable-hover tbody tr:hover {
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+.lightable-minimal.lightable-striped tbody tr:nth-child(even) {
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+
diff --git a/docs/articles/QC_Plots.html b/docs/articles/QC_Plots.html
index d7b953d1a5..c99afae325 100644
--- a/docs/articles/QC_Plots.html
+++ b/docs/articles/QC_Plots.html
@@ -5,21 +5,20 @@
 
 
 
-Plotting #2: QC Plots • scCustomize
-
+Plotting #2: QC Plots & Analysis • scCustomize
+
 
 
 
 
-
-
+
 
 
 
-    
+
 
     
    
       
    
 
@@ -48,7 +47,7 @@
 
  • 
   
   
@@ -128,15 +133,15 @@
 
    • 
 
 
-      
+
 
       
 
    
   
    
     
    
-      
    Plotting #2: QC Plots
    
+      
    Plotting #2: QC Plots & Analysis
    
             
-            
    Compiled: February 28,
+            
    Compiled: December 05,
 2024
    
       
       Source: vignettes/articles/QC_Plots.Rmd
@@ -159,6 +164,9 @@ 
    QC Metrics & PlotsObject
+QC Vignette.
    
 
    For this tutorial, I will be utilizing HCA bone marrow cell data from
 the SeuratData package.
    
     
-
    
-
    Adding QC Metrics
-
    
-
    This is the starting point of nearly every single cell analysis and
-scCustomize contains a number of helper functions to make the process
-fast and easy.
    
-
    
-
    
-
    Add Mitochondrial and Ribosomal Gene Percentages
-
    
-
    scCustomize contains easy wrapper function to automatically add both
-Mitochondrial and Ribosomal count percentages to meta.data slot. If you
-are using mouse, human, rat, zebrafish, drosophila, marmoset, or macaque
-data all you need to do is specify the species
-parameter.
    
 
    -# These defaults can be run just by providing accepted species name
-hca_bm <- Add_Mito_Ribo(object = hca_bm, species = "Human")
    
-
    NOTE: This function works seemlessly for both Seurat and LIGER
-objects.
    
-To view list of accepted values for default species names simply set
-list_species_names = TRUE.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
    
-Mouse_Options
-
-Human_Options
-
-Marmoset_Options
-
-Zebrafish_Options
-
-Rat_Options
-
-Drosophila_Options
-
-Macaque_Options
-
    
-Mouse
-
-Human
-
-Marmoset
-
-Zebrafish
-
-Rat
-
-Drosophila
-
-Macaque
-
    
-mouse
-
-human
-
-marmoset
-
-zebrafish
-
-rat
-
-drosophila
-
-macaque
-
    
-Ms
-
-Hu
-
-CJ
-
-DR
-
-RN
-
-DM
-
-Rhesus
-
    
-ms
-
-hu
-
-Cj
-
-Dr
-
-Rn
-
-Dm
-
-macaca
-
    
-Mm
-
-Hs
-
-cj
-
-dr
-
-rn
-
-dm
-
-mmulatta
-
    
-mm
-
-hs
-
-NA
-
-NA
-
-NA
-
-NA
-
-NA
-
    
-
    However custom prefixes can be used for non-human/mouse/marmoset
-species with different annotations. Simply specify
-species = other and supply feature lists or regex patterns
-for your species of interest.
    NOTE: If desired please submit issue on GitHub for additional
-default species. Please include regex pattern or list of genes for both
-mitochondrial and ribosomal genes and I will add additional built-in
-defaults to the function.
    
-
    -# Using gene name patterns
-hca_bm <- Add_Mito_Ribo(object = hca_bm, species = "other", mito_pattern = "regexp_pattern", ribo_pattern = "regexp_pattern")
-
-# Using feature name lists
-mito_gene_list <- c("gene1", "gene2", "etc")
-ribo_gene_list <- c("gene1", "gene2", "etc")
-hca_bm <- Add_Mito_Ribo(object = hca_bm, species = "other", mito_features = mito_gene_list, ribo_features = ribo_gene_list)
-
-# Using combination of gene lists and gene name patterns
-hca_bm <- Add_Mito_Ribo(object = hca_bm, species = "Human", mito_features = mito_gene_list, ribo_pattern = "regexp_pattern")
    
-
    
-
    Use of Ensembl IDs
-
    
-
    scCustomize contains built in list of ensembl IDs that correspond to
-mitochondrial and ribosomal genes for all default species. If your
-object using ensembl IDs as features names then simply add
-ensembl_ids parameter.
    
-
    -# Using gene name patterns
-hca_bm <- Add_Mito_Ribo(object = hca_bm, species = "Human", ensembl_ids = TRUE)
    
-
    
-
    
-
    
-
    Add Cell Complexity/Novelty QC Metrics
-
    
-
    In addition to metrics like number of features and UMIs it can often
-be helpful to analyze the complexity of expression within a single cell.
-scCustomize provides functions to add two of these metrics to meta
-data.
    
-
    
-
    Cell Complexity (log10(nFeature) / log10(nCount))
-
    
-
    scCustomize contains easy shortcut function to add a measure of cell
-complexity/novelty that can sometimes be useful to filter low quality
-cells. The metric is calculated by calculating the result of
-log10(nFeature) / log10(nCount).
    
-
    -# These defaults can be run just by providing accepted species name
-hca_bm <- Add_Cell_Complexity(object = hca_bm)
    
-
    NOTE: This function works seemlessly for both Seurat and LIGER
-objects.
    
-
    
-
    
-
    Add Top Percent Expression QC Metric
-
    
-
    Additionally, (or alternatively), scCustomize contains another metric
-of complexity which is the top percent expression. The user supplies an
-integer value for num_top_genes (default is 50) which
-species the number of genes and the function returns percentage of
-counts occupied by top XX genes in each cell.
    
-
    -# These defaults can be run just by providing accepted species name
-hca_bm <- Add_Top_Gene_Pct_Seurat(seurat_object = hca_bm, num_top_genes = 50)
    
-
    
-
    
-
    
-
    Add QC Metrics from Pathway Gene Lists
-
    
-
    In addition to those standard QC metrics it can be helpful when using
-network based QC analysis to add the percent of expression of genes
-related to common pathways. This function and the network-based analysis
-is further extension of the analysis/QC from our recent publication:
-Gazestani & Kamath et al., 2023 (Cell).
    
-
    In scCustomize the percent of gene expression from the following gene
-lists can be added as part of the Add_Cell_QC_Metrics (see
-next section for more details):
    
-
      
-
    • Immediate Early Genes (for human and mouse only)
-
        
-
      • Can be used in part to examine potential impact of dissociation or
-post-mortem signatures (Marsh et al.,
-2022) or to identify acutely perturbed populations (gene list
-from Wu et
-al., 2017)
        • 
-
      
-
      • 
-
    • Oxidative Phosphorylation, Apoptosis, & DNA Repair (all default
-species except Marmoset)
-
-
      • 
-
    
-
    
-
    
-
    Add All Cell QC Metrics with Single Function
-
    
-
    To simplify the process of adding cell QC metrics scCustomize
-contains a wrapper function which can be customized to add all or some
-of the available QC metrics. The default parameters of the function
-Add_Cell_QC_Metrics will add:
    
-
      
-
    • Mitochondrial and Ribosomal Percentages (default and custom
-species).
      • 
-
    • Cell Complexity (log10(nFeature) / log10(nCount).
      • 
-
    • Top XX Gene Percentage.
      • 
-
    • Percentage of counts for IEG (human and mouse only).
      • 
-
    • OXPHOS, APOP, and DNA Repair pathways (supported species only).
      • 
-
    • Cell Cycle Scoring (Human only).
      • 
-
    
-
    -hca_bm <- Add_Cell_QC_Metrics(seurat_object = hca_bm, species = "human")
    
-
    
-
    Customizing metrics
-
    
-
    By changing the function parameters you can add a subset of available
-QC metrics. For instance:
    
-
    -hca_bm <- Add_Cell_QC_Metrics(seurat_object = hca_bm, species = "human", add_mito_ribo = TRUE, add_complexity = FALSE,
-    add_top_pct = TRUE, add_IEG = TRUE, add_MSigDB = FALSE, add_cell_cycle = FALSE)
    
-
    
-
    
+hca_bm <- Add_Cell_QC_Metrics(object = hca_bm, species = "human")
    
 
    
 
    Plotting QC Metrics
 
    
@@ -532,15 +233,15 @@ 
    
 
  • Added high/low cutoff parameters to allow for easy visualization of
 potential cutoff thresholds.
    • 
 
-
    +
     # All functions contain
 p1 <- QC_Plots_Genes(seurat_object = hca_bm, low_cutoff = 600, high_cutoff = 5500)
 p2 <- QC_Plots_UMIs(seurat_object = hca_bm, low_cutoff = 1200, high_cutoff = 45000)
 p3 <- QC_Plots_Mito(seurat_object = hca_bm, high_cutoff = 20)
 p4 <- QC_Plots_Complexity(seurat_object = hca_bm, high_cutoff = 0.8)
    
-
    +
     wrap_plots(p1, p2, p3, p4, ncol = 4)
    
-
    
+
    
 
    
 
    Additional parameters
 
    
@@ -568,20 +269,20 @@ 
    Additional parameters
 plot_boxplot: Plot boxplot on top of the violin.
 
-
    +
     p1 <- QC_Plots_UMIs(seurat_object = hca_bm, low_cutoff = 1200, high_cutoff = 45000, pt.size = 0.1)
 p2 <- QC_Plots_UMIs(seurat_object = hca_bm, low_cutoff = 1200, high_cutoff = 45000, pt.size = 0.1,
     y_axis_log = TRUE)
 
 wrap_plots(p1, p2, ncol = 2)
    
 
    
-*Setting `y_axis_log` can be very helpful for initial plots where outliers skew the visualization of the majority of the data without excluding data by setting y-axis limit.*
    
+*Setting `y_axis_log` can be very helpful for initial plots where outliers skew the visualization of the majority of the data without excluding data by setting y-axis limit.*
    
 Setting y_axis_log can be very helpful for initial
 plots where outliers skew the visualization of the majority of the data
 without excluding data by setting y-axis limit.
 
    
 
    
-
    +
     p1 <- QC_Plots_UMIs(seurat_object = hca_bm, low_cutoff = 1200, high_cutoff = 45000, pt.size = 0,
     plot_median = TRUE)
 p2 <- QC_Plots_UMIs(seurat_object = hca_bm, low_cutoff = 1200, high_cutoff = 45000, pt.size = 0,
@@ -589,12 +290,12 @@ 
    Additional parameters
 wrap_plots(p1, p2, ncol = 2)
    
 
    
-*Plotting median values by setting the `plot_median = TRUE` parameter.*
    
+*Plotting median values by setting the `plot_median = TRUE` parameter.*
    
 Plotting median values by setting the
 plot_median = TRUE parameter.
 
    
 
    
-
    +
     p1 <- QC_Plots_UMIs(seurat_object = hca_bm, low_cutoff = 1200, high_cutoff = 45000, pt.size = 0,
     plot_boxplot = TRUE)
 p2 <- QC_Plots_UMIs(seurat_object = hca_bm, low_cutoff = 1200, high_cutoff = 45000, pt.size = 0,
@@ -602,7 +303,7 @@ 
    Additional parameters
 wrap_plots(p1, p2, ncol = 2)
    
 
    
-*Plotting boxplot by setting the `plot_boxplot = TRUE` parameter.*
    
+*Plotting boxplot by setting the `plot_boxplot = TRUE` parameter.*
    
 Plotting boxplot by setting the plot_boxplot = TRUE
 parameter.
 
    
@@ -614,10 +315,10 @@ 
    Combined Plotting FunctionAs a shortcut you can return single patchwork plot of the 3 main QC
 Plots (Genes, UMIs, %Mito) by using single function,
 QC_Plots_Combined_Vln().
    
-
    +
     QC_Plots_Combined_Vln(seurat_object = hca_bm, feature_cutoffs = c(600, 5500), UMI_cutoffs = c(1200,
     45000), mito_cutoffs = 20, pt.size = 0.1)
    
-
    
+
    
 
    
 
    
 
    
@@ -655,13 +356,13 @@ 
    New/Modified functionalityQC_Plot_UMIvsGene (based on
 values provided to high and low cutoff parameters)
 
-
    +
     # All functions contain
 QC_Plot_UMIvsGene(seurat_object = hca_bm, low_cutoff_gene = 600, high_cutoff_gene = 5500, low_cutoff_UMI = 500,
     high_cutoff_UMI = 50000)
 QC_Plot_GenevsFeature(seurat_object = hca_bm, feature1 = "percent_mito", low_cutoff_gene = 600,
     high_cutoff_gene = 5500, high_cutoff_feature = 20)
    
-
    
+
    
 
    
 
    
 
    Color data by continuous meta data variable
@@ -670,13 +371,13 @@ 
    Color data by continuous me
 by continuous meta data variables.
    
 This can be used to plot % of mito reads in addition to UMI vs. Gene
 comparisons
    
-
    +
     QC_Plot_UMIvsGene(seurat_object = hca_bm, meta_gradient_name = "percent_mito", low_cutoff_gene = 600,
     high_cutoff_gene = 5500, high_cutoff_UMI = 45000)
 QC_Plot_UMIvsGene(seurat_object = hca_bm, meta_gradient_name = "percent_mito", low_cutoff_gene = 600,
     high_cutoff_gene = 5500, high_cutoff_UMI = 45000, meta_gradient_low_cutoff = 20)
    
 
    
-*`QC_Plot_UMIvsGene()` when using `meta_gradient_name` outputs plot colored by meta data variable (left) to view only points above potential cutoff `meta_gradient_low_cutoff` can be specified to alter the plotting (right).*
    
+*`QC_Plot_UMIvsGene()` when using `meta_gradient_name` outputs plot colored by meta data variable (left) to view only points above potential cutoff `meta_gradient_low_cutoff` can be specified to alter the plotting (right).*
    
 QC_Plot_UMIvsGene() when using
 meta_gradient_name outputs plot colored by meta data
 variable (left) to view only points above potential cutoff
@@ -692,11 +393,11 @@ 
    Combination Plots
    +
     QC_Plot_UMIvsGene(seurat_object = hca_bm, meta_gradient_name = "percent_mito", low_cutoff_gene = 600,
     high_cutoff_gene = 5500, high_cutoff_UMI = 45000, meta_gradient_low_cutoff = 20, combination = TRUE)
    
 
    
-*`QC_Plot_UMIvsGene()` when using `combination = TRUE` will output both the Gene x UMI by active identity and with meta data gradient coloring.*
    
+*`QC_Plot_UMIvsGene()` when using `combination = TRUE` will output both the Gene x UMI by active identity and with meta data gradient coloring.*
    
 QC_Plot_UMIvsGene() when using
 combination = TRUE will output both the Gene x UMI by
 active identity and with meta data gradient coloring.
@@ -710,13 +411,13 @@ 
    Histogram-Based QC PlotsFinally, scCustomize contains a function to plot QC metrics as
 histogram instead of violin for visualization of the distribution of
 feature.
    
-
    +
     QC_Histogram(seurat_object = hca_bm, features = "percent_mito", low_cutoff = 15)
    
-
    
-
    +
    
+
     QC_Histogram(seurat_object = hca_bm, features = "percent_mito", low_cutoff = 15, split.by = "group")
    
 
    
-*`QC_Histogram` also supports splitting plots by meta.data variables*
    
+*`QC_Histogram` also supports splitting plots by meta.data variables*
    
 QC_Histogram also supports splitting plots by meta.data
 variables
 
    
@@ -734,7 +435,7 @@ 
    Calculate Median Values &
 
    scCustomize contains function Median_Stats to quickly
 calculate the medians for basic QC stats (Genes/, UMIs/, %Mito/Cell,
 etc) and return a data.frame.
    
-
    +
     median_stats <- Median_Stats(seurat_object = hca_bm, group_by_var = "orig.ident")
    
 
@@ -973,7 +674,7 @@ 
    Calculate Median Values &
 
    The Median_Stats function has some column names stored
 by default but will also calculate medians for additional meta.data
 columns using the optional median_var parameter
    
-
    +
     median_stats <- Median_Stats(seurat_object = hca_bm, group_by_var = "orig.ident", median_var = "meta_data_column_name")
    
 
    
 
    
@@ -1000,12 +701,12 @@ 
    Plotting Median Values
 
 
-
    +
     Plot_Median_Genes(seurat_object = hca_bm, group_by = "group")
 Plot_Median_UMIs(seurat_object = hca_bm, group_by = "group")
 Plot_Median_Mito(seurat_object = hca_bm, group_by = "group")
 Plot_Median_Other(seurat_object = hca_bm, median_var = "percent_ribo", group_by = "group")
    
-
    
+
    
 
    
 
    
 
    Plot Number of Cells/Nuclei per Sample
@@ -1015,7 +716,7 @@ 
    Plot Number of Cells/Nuclei per S
 
    Since the HCA Bone Marrow dataset has exactly the same number of
 cells per sample we will use the microglia object from the Analysis
 Plots vignette.
    
-
    
+
    
 
    
 
    
 
@@ -1023,9 +724,7 @@ 
    Plot Number of Cells/Nuclei per S
 
   
+      
 
 
 
@@ -1038,16 +737,16 @@ 
    Plot Number of Cells/Nuclei per S
 
 
    
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
 
-  
 
 
-  
+
+
 
   
 
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diff --git a/docs/articles/Read_and_Write_Functions.html b/docs/articles/Read_and_Write_Functions.html
index 3af8f7d591..5372ab6def 100644
--- a/docs/articles/Read_and_Write_Functions.html
+++ b/docs/articles/Read_and_Write_Functions.html
@@ -6,20 +6,19 @@
 
 
 Read & Write Data Functions • scCustomize
-
+
 
 
 
 
 
-
 
 
 
-    
+
 
     
    
       
    
 
@@ -48,7 +47,7 @@
 
  • 
   
   
@@ -128,14 +133,14 @@
 
    • 
 
 
-      
+
 
       
    
   
    
     
    
       
    Read & Write Data Functions
    
             
-            
    Compiled: February 28,
+            
    Compiled: December 05,
 2024
    
       
       Source: vignettes/articles/Read_and_Write_Functions.Rmd
@@ -472,7 +477,7 @@ 
    Write 10X Genomi
 
    Create_10X_H5 provides convenient wrapper around
 write10xCounts() from DropletUtils package. Output can then
 be easily read in using Seurat::Read10X_h5() or LIGER’s
-createLiger() (which assumes H5 file is formatted as if
+createLiger() (which assumes H5 file is formatted as if
 from Cell Ranger).
    
 
     # Provide file path and specify type of files as either cell ranger triplicate files, matrix,
@@ -485,9 +490,7 @@ 
    Write 10X Genomi
 
   
+      
    
 
 
    
 
@@ -500,16 +503,16 @@ 
    Write 10X Genomi
 
 
    
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/articles/Sequencing_QC_Plots.html b/docs/articles/Sequencing_QC_Plots.html
index ef70a9dc9e..93032d1474 100644
--- a/docs/articles/Sequencing_QC_Plots.html
+++ b/docs/articles/Sequencing_QC_Plots.html
@@ -6,20 +6,19 @@
 
 
 Plotting #3: Sequencing QC Plots/Analysis • scCustomize
-
+
 
 
 
 
 
-
 
 
 
-    
+
 
     
    
       
    
 
@@ -48,7 +47,7 @@
 
  • 
   
   
@@ -128,7 +133,7 @@
 
    • 
 
 
-      
+
 
       
 
    
@@ -136,7 +141,7 @@
     
    
       
    Plotting #3: Sequencing QC Plots/Analysis
    
             
-            
    Compiled: February 28,
+            
    Compiled: December 05,
 2024
    
       
       Source: vignettes/articles/Sequencing_QC_Plots.Rmd
@@ -168,7 +173,7 @@ 
    Plotting Sequencing/Alignment Metr
 library(magrittr)
 library(Seurat)
 library(scCustomize)
-library(qs)
    
+library(qs)
    
 
    
 
    Loading Data
 
    
@@ -879,9 +884,7 @@ 
    Barcode Rank Plots
 
-        
-
    
+      
    
 
 
 
@@ -894,16 +897,16 @@ 
    Barcode Rank Plots
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.0.
    
 
 
       
 
 
-  
 
 
-  
+
+
 
   
 
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diff --git a/docs/articles/Spatial_Plotting.html b/docs/articles/Spatial_Plotting.html
new file mode 100644
index 0000000000..b477721a9c
--- /dev/null
+++ b/docs/articles/Spatial_Plotting.html
@@ -0,0 +1,259 @@
+
+
+
+
+
+
+
+Plotting #5: Spatial Plotting Functions • scCustomize
+
+
+
+
+
+
+
+
+
+
+
+    
    
+      
    
+
+
+
+
+      
    
+  
    
+    
    
+      
    Plotting #5: Spatial Plotting Functions
    
+            
+            
    Compiled: December 05,
+2024
    
+      
+      Source: vignettes/articles/Spatial_Plotting.Rmd
+      
+
+    
    
+
+    
+    
+
    
+
+
    
+
    Customizing Plots for Enhanced/Simplified Visualization in Spatial
+Analyses
+
    
+
    While the default plots from Seurat and other packages are often very
+good they are often modified from their original outputs after plotting.
+scCustomize seeks to simplify this process and enhance some of the
+default visualizations.
    
+
    For this tutorial, I will be utilizing two spatial datasets to
+illustrate scCustomize functions (both are part of SeuratData
+package).
    
+
    +library(ggplot2)
+library(dplyr)
+library(magrittr)
+library(patchwork)
+library(viridis)
+library(Seurat)
+library(scCustomize)
+library(qs)
+
+# Load stxBrain Visium dataset and Slide-seq V2 ssHippo dataset
+mouse_ctx <- SeuratData::LoadData("stxBrain", type = "anterior1")
+
+slide.seq <- SeuratData::LoadData("ssHippo")
    
+
    
+
    In order to be compatible with this vignette we will follow Seurat
+vignette processing of this data.
+
    
+
    +# Visium
+mouse_ctx <- SCTransform(mouse_ctx, assay = "Spatial", verbose = FALSE)
+mouse_ctx <- RunPCA(mouse_ctx, assay = "SCT", verbose = FALSE)
+mouse_ctx <- FindNeighbors(mouse_ctx, reduction = "pca", dims = 1:30)
+mouse_ctx <- FindClusters(mouse_ctx, verbose = FALSE)
+mouse_ctx <- RunUMAP(mouse_ctx, reduction = "pca", dims = 1:30)
+
+# Slide-seq
+slide.seq <- SCTransform(slide.seq, assay = "Spatial", ncells = 3000, verbose = FALSE)
+slide.seq <- RunPCA(slide.seq)
+slide.seq <- RunUMAP(slide.seq, dims = 1:30)
+slide.seq <- FindNeighbors(slide.seq, dims = 1:30)
+slide.seq <- FindClusters(slide.seq, resolution = 0.3, verbose = FALSE)
    
+
    
+
    
+
    Spatial DimPlots
+
    
+
    Currently, spatial support in scCustomize is limited to one plotting
+function SpatialDimPlot. scCustomize provides a matching
+scCustomize version of the function:
+SpatialDimPlot_scCustom to align these plots with
+scCustomize style and colors.
    NOTE: If you are interested in further spatial functionality within
+scCustomize please post issue to GitHub or directly submit PR, as future
+implementations will be based on user demand.
    
+
    The issue with the default SpatialDimPlot are similar to
+those affecting the regular DimPlot. Namely that the
+default color scheme can make it very difficult to tell spot colors from
+each other. SpatialDimPlot_scCustom() solves these
+issues.
    
+
    
+***A.** Default plotting results in colors that are very similar between clusters making it hard to differentiate between them on the image.  **B.** Default plot using scCustomize `SpatialDimPlot_scCustom` solves this issues matching color scheme to scCustomize package defaults.*
    
+A. Default plotting results in colors that are very
+similar between clusters making it hard to differentiate between them on
+the image. B. Default plot using scCustomize
+SpatialDimPlot_scCustom solves this issues matching color
+scheme to scCustomize package defaults.
+
    
+
    
+
    
+
    
+
    
+  
    
+
+  
+
+
    
+
+
+
+      
    
+  
    
+
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    
+
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
    
+
+
+
+
+
+
+  
+
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diff --git a/docs/articles/Statistics.html b/docs/articles/Statistics.html
index 4b90389f8c..0a4a9bf8d2 100644
--- a/docs/articles/Statistics.html
+++ b/docs/articles/Statistics.html
@@ -6,20 +6,19 @@
 
 
 Statistics Functions • scCustomize
-
+
 
 
 
 
 
-
 
 
 
-    
+
 
     
    
       
    
 
@@ -48,7 +47,7 @@
 
  • 
   
   
@@ -128,7 +133,7 @@
 
    • 
 
 
-      
+
 
       
 
    
@@ -136,7 +141,7 @@
     
    
       
    Statistics Functions
    
             
-            
    Compiled: February 28,
+            
    Compiled: December 05,
 2024
    
       
       Source: vignettes/articles/Statistics.Rmd
@@ -162,11 +167,12 @@ 
    Statistics Functions
     # Load Packages
 library(ggplot2)
+library(patchwork)
 library(dplyr)
 library(magrittr)
 library(Seurat)
 library(scCustomize)
-library(qs)
+library(qs)
 
 # Load example dataset for tutorial
 pbmc <- pbmc3k.SeuratData::pbmc3k.final
    
@@ -180,6 +186,11 @@ 
    Statistics Functionspbmc@meta.data$group[pbmc@meta.data$orig.ident == "sample1" | pbmc@meta.data$orig.ident == "sample3"] <- "Group 1"
 pbmc@meta.data$group[pbmc@meta.data$orig.ident == "sample2" | pbmc@meta.data$orig.ident == "sample4"] <- "Group 2"
 
+
+pbmc@meta.data$treatment[pbmc@meta.data$orig.ident == "sample1"] <- "Control"
+pbmc@meta.data$treatment[pbmc@meta.data$orig.ident == "sample2" | pbmc@meta.data$orig.ident == "sample4" |
+    pbmc@meta.data$orig.ident == "sample3"] <- "Treated"
+
 # Add dummy module score
 pbmc <- AddModuleScore(object = pbmc, features = list(c("CD3E", "CD4", "THY1", "TCRA")), name = "module_score")
    
 
    
@@ -241,28 +252,28 @@ 
    Cells Per Identity
-178
+182
 
 
    
@@ -276,28 +287,28 @@ 
    Cells Per Identity
-124
+141
 
 
    
@@ -311,28 +322,28 @@ 
    Cells Per Identity
-134
+118
 
 
    
@@ -346,28 +357,28 @@ 
    Cells Per Identity
-106
+79
 
 
    
@@ -381,28 +392,28 @@ 
    Cells Per Identity
-62
+60
 
 
    
@@ -416,28 +427,28 @@ 
    Cells Per Identity
-31
+42
 
 
    
@@ -451,28 +462,28 @@ 
    Cells Per Identity
-44
+43
 
 
    
@@ -489,25 +500,25 @@ 
    Cells Per Identity
-6
-
-
    
+
@@ -521,28 +532,28 @@ 
    Cells Per Identity
-4
+3
 
 
    
@@ -556,16 +567,16 @@ 
    Cells Per Identity
-690
+675
 
 
    
@@ -648,16 +659,16 @@ 
    Cells Per Identity
-241
+253
 
 
    
@@ -671,16 +682,16 @@ 
    Cells Per Identity
-249
+235
 
 
    
@@ -694,16 +705,16 @@ 
    Cells Per Identity
-189
+157
 
 
    
@@ -717,16 +728,16 @@ 
    Cells Per Identity
-144
+138
 
 
    
@@ -740,16 +751,16 @@ 
    Cells Per Identity
-78
+82
 
 
    
@@ -763,16 +774,16 @@ 
    Cells Per Identity
-72
+84
 
 
    
@@ -786,16 +797,16 @@ 
    Cells Per Identity
-17
+16
 
 
    
@@ -809,16 +820,16 @@ 
    Cells Per Identity
-9
+7
 
 
    
@@ -832,10 +843,10 @@ 
    Cells Per Identity
-1348
+1333
 
 
    
 
    
-189
+176
 
 
-171
+179
 
 
-159
+160
 
 
-25.7971014
+26.9629630
 
 
-29.0322581
+26.3079223
 
 
-25.9878419
+27.2036474
 
 
-24.8826291
+25.1572327
 
 
    
 
    
-122
+127
 
 
-117
+112
 
 
-120
+103
 
 
-17.9710145
+20.8888889
 
 
-18.7403994
+18.9835575
 
 
-17.7811550
+17.0212766
 
 
-18.7793427
+16.1949686
 
 
    
 
    
-114
+126
 
 
-115
+117
 
 
-117
+119
 
 
-19.4202899
+17.4814815
 
 
-17.5115207
+18.8340807
 
 
-17.4772036
+17.7811550
 
 
-18.3098592
+18.7106918
 
 
    
 
    
-67
+90
 
 
-83
+78
 
 
-88
+97
 
 
-15.3623188
+11.7037037
 
 
-10.2918587
+13.4529148
 
 
-12.6139818
+11.8541033
 
 
-13.7715180
+15.2515723
 
 
    
 
    
 65
 
 
-82
+78
 
 
-62
+68
 
 
-8.9855072
+8.8888889
 
 
-9.9846390
+9.7159940
 
 
-12.4620061
+11.8541033
 
 
-9.7026604
+10.6918239
 
 
    
 
    
-45
+34
 
 
-47
+40
 
 
-39
+46
 
 
-4.4927536
+6.2222222
 
 
-6.9124424
+5.0822123
 
 
-7.1428571
+6.0790274
 
 
-6.1032864
+7.2327044
 
 
    
 
    
-42
+37
 
 
-28
+41
 
 
-41
+34
 
 
-6.3768116
+6.3703704
 
 
-6.4516129
+5.5306428
 
 
-4.2553191
+6.2310030
 
 
-6.4162754
+5.3459119
 
 
    
 
    
 10
 
 
 9
 
 
-1.0144928
+6
 
 
-0.9216590
+1.0370370
 
 
-1.5197568
+1.4947683
 
 
-1.4084507
+1.3677812
+
+0.9433962
 
 
    
 
    
-1
+4
 
 
-5
+4
 
 
-4
+3
 
 
-0.5797101
+0.4444444
 
 
-0.1536098
+0.5979073
 
 
-0.7598784
+0.6079027
 
 
-0.6259781
+0.4716981
 
 
    
 
    
-651
+669
 
 
 658
 
 
-639
+636
 
 
 100.0000000
@@ -625,16 +636,16 @@ 
    Cells Per Identity
-349
+361
 
    		
 
-348
+336
 
 
-25.8902077
+27.0817704
 
 
-26.9767442
+25.7471264
 
 
    
 
    
-242
+230
 
 
-17.8783383
+18.9797449
 
 
-18.7596899
+17.6245211
 
 
    
 
    
-231
+245
 
 
-18.4718101
+17.6294074
 
 
-17.9069767
+18.7739464
 
 
    
 
    
-155
+187
 
 
-14.0207715
+11.7779445
 
 
-12.0155039
+14.3295019
 
 
    
 
    
-127
+133
 
 
-10.6824926
+10.3525881
 
 
-9.8449612
+10.1915709
 
 
    
 
    
-84
+80
 
 
-5.7863501
+6.1515379
 
 
-6.5116279
+6.1302682
 
 
    
 
    
-83
+71
 
 
-5.3412463
+6.3015754
 
 
-6.4341085
+5.4406130
 
 
    
 
    
-15
+16
 
 
-1.2611276
+1.2003001
 
 
-1.1627907
+1.2260536
 
 
    
 
    
-5
+7
 
 
-0.6676558
+0.5251313
 
 
-0.3875969
+0.5363985
 
 
    
 
    
-1290
+1305
 
 
 100.0000000
@@ -848,13 +859,63 @@ 
    Cells Per Identity
+
    Plotting Cluster/Identity Proportions
+
    
+
    Understanding the proportion of cells per cluster and how that may
+change across a group can be important aspect of single cell analysis.
+scCustomize contains function Proportion_Plot to provide
+some visualization of cell proportions.
    
+
    Plotting proportionality can be tricky especially when dealing with
+clusters of very disparate sizes (especially small clusters) so plese be
+aware to examine raw data as well (see
+Cluster_Stats_All_Samples()).
    
+
    Also note that when splitting plot by group there are now error bars
+on these plots for interpretation of variance and other plotting methods
+should be used to convery such information.
    
+
    
+
    Basic Proportion Plots
+
    
+
    Proportion_Plot can either return a bar graph or pie
+graph depending on parameter value for
    
+
    +Proportion_Plot(seurat_object = pbmc, plot_type = "bar")
+
+Proportion_Plot(seurat_object = pbmc, plot_type = "pie")
    
+
    
+
    
+
    
+
    Plot across groups
+
    
+
    Like other plots you can also use Proportion_Plot to
+split plot across any categorical meta.data variable.
    
+
    +Proportion_Plot(seurat_object = pbmc, plot_type = "bar", split.by = "treatment")
    
+
    
+
    +Proportion_Plot(seurat_object = pbmc, plot_type = "pie", split.by = "treatment")
    
+
    
+
    
+
    
+
    Plot raw cell numbers
+
    
+
    The default for Proportion_Plot is to plot the
+proportion of cells and not the raw number of cells per identity because
+that can be deceptive. However, in some cases it can be useful and so
+users can change the plot_scale parameter to plot raw
+numbers of cells instead of proportions.
    
+
    +Proportion_Plot(seurat_object = pbmc, plot_type = "bar", split.by = "treatment", plot_scale = "count")
    
+
    
+
    
+
+
    
 
    Percent of Cells Expressing Feature(s)
 
    
 
    It can also be informative to understand the percent of cells/nuclei
 that express a given feature or set of features.
    
 scCustomize provides the Percent_Expressing function to
 return these results.
    
-
    +
     percent_express <- Percent_Expressing(seurat_object = pbmc, features = c("CD4", "CD8A"))
    
 
@@ -961,23 +1022,23 @@ 
    Change grouping variableBy default the function groups expression across
 @active.ident (see above) but user can specify difference
 variable if desired.
    
-
    +
     percent_express <- Percent_Expressing(seurat_object = pbmc, features = c("CD4", "CD8A"), group_by = "orig.ident")
    
 
    
 
    
@@ -986,16 +1047,16 @@ 
    Change grouping variable
 
    
@@ -1003,16 +1064,16 @@ 
    Change grouping variable
 
    
@@ -1023,17 +1084,17 @@ 
    Split within groups
    +
     percent_express <- Percent_Expressing(seurat_object = pbmc, features = c("CD4", "CD8A"), split_by = "group")
    
 
    
 
    
 
 
 
-sample2
+sample3
 
 
-sample4
+sample1
 
 
-sample1
+sample4
 
 
-sample3
+sample2
 
 
    
 
    
-14.28571
+11.39818
 
 
-9.076682
+11.55556
 
 
-10.72464
+11.79245
 
 
-12.76596
+12.10762
 
 
    
 
    
-11.98157
+12.91793
 
 
-10.172144
+12.74074
 
 
-12.02899
+11.00629
 
 
-12.91793
+10.46338
 
 
    
 
    
 
    
 
 
 
-Naive.CD4.T_Group.2
+Naive.CD4.T_Group.1
 
 
-Naive.CD4.T_Group.1
+Naive.CD4.T_Group.2
 
 
 Memory.CD4.T_Group.1
@@ -1048,10 +1109,10 @@ 
    Split within groups
-B_Group.2
+B_Group.1
 
    		
 
-B_Group.1
+B_Group.2
 
 
 CD8.T_Group.1
@@ -1060,10 +1121,10 @@ 
    Split within groups
-FCGR3A..Mono_Group.1
+FCGR3A..Mono_Group.2
 
    		
 
-FCGR3A..Mono_Group.2
+FCGR3A..Mono_Group.1
 
 
 NK_Group.1
@@ -1090,52 +1151,52 @@ 
    Split within groups
-7.758621
+6.371191
 
 
    		
-5.730659
+7.142857
 
 
-15.767635
+17.39130
 
 
-16.11570
+14.347826
 
 
-25.702811
+24.255319
 
 
-22.943723
+24.48980
 
 
-1.290323
+0.000000
 
 
-1.587302
+2.673797
 
 
-3.472222
+3.623188
 
 
-1.574803
+1.503759
 
 
-25.641026
+31.25
 
 
-28.571429
+23.170732
 
 
-1.388889
+0.000000
 
 
-0.00000
+1.408451
 
 
-26.666667
+37.5
 
 
-41.17647
+31.25
 
 
 0
@@ -1149,52 +1210,52 @@ 
    Split within groups
-12.643678
+13.573407
 
    		
 
-14.040115
+13.095238
 
 
-9.958506
+10.67194
 
 
-7.85124
+6.956522
 
 
-2.008032
+2.553192
 
 
-1.731602
+1.22449
 
 
-2.580645
+1.273885
 
 
-2.645503
+3.743316
 
 
-56.250000
+55.797101
 
 
-44.094488
+45.112782
 
 
-1.282051
+3.75
 
 
-5.952381
+3.658537
 
 
-4.166667
+7.142857
 
 
-12.04819
+9.859155
 
 
-6.666667
+0.0
 
 
-0.00000
+6.25
 
 
 0
@@ -1214,7 +1275,7 @@ 
    Set threshold of expression
    +
     percent_express <- Percent_Expressing(seurat_object = pbmc, features = c("CD4", "CD8A"), threshold = 2)
    
 
@@ -1329,7 +1390,7 @@ 
    Basic Use
    +
     median_stats <- Median_Stats(seurat_object = pbmc, group_by_var = "orig.ident")
    
 
    
 
    
@@ -1358,19 +1419,19 @@ 
    Basic Use
-2189.0
+2193
 
 
    
@@ -1378,19 +1439,19 @@ 
    Basic Use
-2193.0
+2178
 
 
    
@@ -1398,19 +1459,19 @@ 
    Basic Use
-2204.5
+2241
 
 
    
@@ -1418,19 +1479,19 @@ 
    Basic Use
-2250.0
+2251
 
 
    
@@ -1438,7 +1499,7 @@ 
    Basic Use
-2213.0
+2213
 
 
    
 
    
-810.0
+813.0
 
 
-2.045561
+2.005731
 
 
-37.30009
+36.91964
 
 
-39.50258
+39.08969
 
 
    
 
    
-817.0
+812.0
 
 
-1.937208
+2.016383
 
 
-36.68319
+37.03217
 
 
-39.02439
+39.31227
 
 
    
 
    
-821.5
+820.0
 
 
-2.006391
+1.982099
 
 
-36.89451
+37.40017
 
 
-38.77124
+39.24930
 
 
    
 
    
-829.0
+836.5
 
 
-2.076271
+2.057405
 
 
-36.90902
+36.16109
 
 
-38.92387
+38.38636
 
 
    
 
    
 819.0
@@ -1463,7 +1524,7 @@ 
    Additional Variables
    +
     median_stats <- Median_Stats(seurat_object = pbmc, group_by_var = "orig.ident", median_var = "module_score1")
    
 
@@ -1495,22 +1556,22 @@ 
    Additional Variables
-2189.0
+2193
 
 
    
@@ -1518,22 +1579,22 @@ 
    Additional Variables
-2193.0
+2178
 
 
    
@@ -1541,22 +1602,22 @@ 
    Additional Variables
-2204.5
+2241
 
 
    
@@ -1564,22 +1625,22 @@ 
    Additional Variables
-2250.0
+2251
 
 
    
@@ -1587,7 +1648,7 @@ 
    Additional Variables
-2213.0
+2213
 
 
    
 
    
-810.0
+813.0
 
 
-2.045561
+2.005731
 
 
-37.30009
+36.91964
 
 
-39.50258
+39.08969
 
 
--0.1551981
+-0.0545099
 
 
    
 
    
-817.0
+812.0
 
 
-1.937208
+2.016383
 
 
-36.68319
+37.03217
 
 
-39.02439
+39.31227
 
 
-0.0076579
+-0.0678532
 
 
    
 
    
-821.5
+820.0
 
 
-2.006391
+1.982099
 
 
-36.89451
+37.40017
 
 
-38.77124
+39.24930
 
 
--0.0939919
+-0.0793297
 
 
    
 
    
-829.0
+836.5
 
 
-2.076271
+2.057405
 
 
-36.90902
+36.16109
 
 
-38.92387
+38.38636
 
 
--0.1788730
+-0.1935054
 
 
    
 
    
 819.0
@@ -1615,7 +1676,7 @@ 
    Calculate Median Absolute Deviatio
 function to calculate the median absolute deviation for each of those
 features with function MAD_Stats. By setting the parameter
 mad_num the function will retrun the MAD*mad_num.
    
-
    +
     mad <- MAD_Stats(seurat_object = pbmc, group_by_var = "orig.ident", mad_num = 2)
    
 
@@ -1644,19 +1705,19 @@ 
    Calculate Median Absolute Deviatio
 sample1
 
 
    
@@ -1664,19 +1725,19 @@ 
    Calculate Median Absolute Deviatio
 sample2
 
 
    
@@ -1684,19 +1745,19 @@ 
    Calculate Median Absolute Deviatio
 sample3
 
 
    
@@ -1704,19 +1765,19 @@ 
    Calculate Median Absolute Deviatio
 sample4
 
 
    
@@ -1724,19 +1785,19 @@ 
    Calculate Median Absolute Deviatio
 Totals (All Cells)
 
 
    
@@ -1754,22 +1815,20 @@ 
    Plotting Median DataPlot_Median_Mito()
 
  • Plot_Median_Other()
    • 
 
-
    +
     Plot_Median_Genes(seurat_object = pbmc)
 
 Plot_Median_Genes(seurat_object = pbmc, group_by = "group")
 
 Plot_Median_Other(seurat_object = pbmc, median_var = "module_score1", group_by = "group")
    
-
    
+
    
 
    
 
   
 
   
+      
 
 
 
@@ -1782,16 +1841,16 @@ 
    Plotting Median Data
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.0.
    
 
 
       
 
 
-  
 
 
-  
+
+
 
   
 
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index 0000000000..55639ce48a
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new file mode 100644
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diff --git a/docs/articles/Statistics_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/Statistics_files/figure-html/unnamed-chunk-9-1.png
new file mode 100644
index 0000000000..1d981d3f31
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diff --git a/docs/articles/Update_Gene_Symbols.html b/docs/articles/Update_Gene_Symbols.html
index b8e2aceebe..d7208ac7ce 100644
--- a/docs/articles/Update_Gene_Symbols.html
+++ b/docs/articles/Update_Gene_Symbols.html
@@ -6,20 +6,19 @@
 
 
 Updating Gene Symbols • scCustomize
-
+
 
 
 
 
 
-
 
 
 
-    
+
 
     
    
       
    
 
@@ -48,7 +47,7 @@
 
  • 
   
   
@@ -128,7 +133,7 @@
 
    • 
 
 
-      
+
 
       
 
    
@@ -136,7 +141,7 @@
     
    
       
    Updating Gene Symbols
    
             
-            
    Compiled: February 28,
+            
    Compiled: December 05,
 2024
    
       
       Source: vignettes/articles/Update_Gene_Symbols.Rmd
@@ -168,12 +173,12 @@ 
    Upating Human Gene Symbols# Load Packages
 library(Seurat)
 library(scCustomize)
-library(qs)
    
+library(qs)
    
 
    Load Seurat Object & Add QC Data
    
 
     # read object
 pbmc <- pbmc3k.SeuratData::pbmc3k.final
-pbmc <- UpdateSeuratObject(pbmc)
    
+pbmc <- UpdateSeuratObject(pbmc)
 
    
 
    Issues with other functions
 
    
@@ -252,7 +257,9 @@ 
    Inappropriate renamingLet’s run our test symbol set:
    
 
     results <- Updated_HGNC_Symbols(input_data = test_symbols)
    
-
    ## Input features contained 3 gene symbols
+
    ## Downloading HGNC data from:
+## https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt
+## Input features contained 3 gene symbols
 ## ✔ 3 were already approved symbols.
 ## → 0 were updated to approved symbol.
 ## ✖ 0 were not found in HGNC dataset and remain unchanged.
    
@@ -343,12 +350,12 @@ 
    Inappropriate renamingtic()
 results <- Updated_HGNC_Symbols(input_data = features)
    
 
    ## Input features contained 36,601 gene symbols
-## ✔ 23,360 were already approved symbols.
-## → 654 were updated to approved symbol.
-## ✖ 12,587 were not found in HGNC dataset and remain unchanged.
    
+## ✔ 23,261 were already approved symbols.
+## → 749 were updated to approved symbol.
+## ✖ 12,591 were not found in HGNC dataset and remain unchanged.
 
     toc()
    
-
    ## 0.654 sec elapsed
    
+
    ## 0.824 sec elapsed
    
 
 
    
 
    Examining the Results
@@ -591,14 +598,31 @@ 
    Examining the Results
 
    
 
+
+
    
+
    Updating Mouse Gene Symbols
+
    
+
    scCustomize also contains helper function to update mouse gene
+symbols using the Mouse
+Genome Informatics (MGI) database.
    
+
    +# Load mouse dataset
+marsh_mouse_micro <- qread(file = "assets/marsh_2020_micro.qs")
+
+# Get updated symbols
+updated_symbols <- Updated_MGI_Symbols(input_data = Features(marsh_mouse_micro))
    
+
    ## Downloading MGI data from:
+## https://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt
+## Input features contained 12,674 gene symbols
+## ✔ 12,055 were already approved symbols.
+## → 531 were updated to approved symbol.
+## ✖ 90 were not found in MGI dataset and remain unchanged.
    
 
    
   
 
   
+      
 
 
 
@@ -611,16 +635,16 @@ 
    Examining the Results
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.0.
    
 
 
       
 
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/articles/articles/Object_QC_Functions.html b/docs/articles/articles/Object_QC_Functions.html
new file mode 100644
index 0000000000..52aec48728
--- /dev/null
+++ b/docs/articles/articles/Object_QC_Functions.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/articles/articles/Spatial_Plotting.html b/docs/articles/articles/Spatial_Plotting.html
new file mode 100644
index 0000000000..ad4f56c761
--- /dev/null
+++ b/docs/articles/articles/Spatial_Plotting.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 0fc34f7fc7..936641050d 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,9 +1,9 @@
 
-Articles • scCustomizeArticles • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -135,12 +141,16 @@ 
    All vignettes
    
         
    
         
    Object Format Conversion
    
         
    
-        
    Plotting #2: QC Plots
    
+        
    Object QC Functions
    
+        
    
+        
    Plotting #2: QC Plots & Analysis
    
         
    
         
    Read & Write Data Functions
    
         
    
         
    Plotting #3: Sequencing QC Plots/Analysis
    
         
    
+        
    Plotting #5: Spatial Plotting Functions
    
+        
    
         
    Statistics Functions
    
         
    
         
    Updating Gene Symbols
    
@@ -155,15 +165,15 @@ 
    All vignettes
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/authors.html b/docs/authors.html
index 384ef8eb91..12eff8b635 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,9 +1,9 @@
 
-Authors and Citation • scCustomizeAuthors and Citation • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
     
    
       
    
-        
    Authors
    
+        
    Authors and Citation
    
       
    
 
-      
+
       
    • 
           
      Samuel Marsh. Author, maintainer. 
           
      
         
      • 
         
    • 
-          
      Ming Tang. Contributor. 
+          
      Ming Tang. Contributor.
           
      
         
      • 
         
    • 
-          
      Velina Kozareva. Contributor. 
+          
      Velina Kozareva. Contributor.
           
      
         
      • 
         
    • 
-          
      Lucas Graybuck. Contributor. 
+          
      Lucas Graybuck. Contributor.
           
      
         
      • 
       
    
@@ -138,13 +144,13 @@ 
    Citation
    
 
     
    Marsh S (2024).
 scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing.
-R package version 2.1.2, https://samuel-marsh.github.io/scCustomize/, https://doi.org/10.5281/zenodo.5706431, https://github.com/samuel-marsh/scCustomize. 
+R package version 3.0.0, https://samuel-marsh.github.io/scCustomize/, https://doi.org/10.5281/zenodo.5706431, https://github.com/samuel-marsh/scCustomize.
 
    
     
    @Manual{,
   title = {scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing},
   author = {Samuel Marsh},
   year = {2024},
-  note = {R package version 2.1.2, https://samuel-marsh.github.io/scCustomize/, https://doi.org/10.5281/zenodo.5706431},
+  note = {R package version 3.0.0, https://samuel-marsh.github.io/scCustomize/, https://doi.org/10.5281/zenodo.5706431},
   url = {https://github.com/samuel-marsh/scCustomize},
 }
    
 
@@ -159,15 +165,15 @@ 
    Citation
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/index.html b/docs/index.html
index e767ecf833..dc4ba2c136 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,20 +6,20 @@
 
 
 Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing • scCustomize
-
+
 
 
 
 
 
-
+
 
 
 
-    
+
 
     
    
       
    
 
@@ -48,7 +48,7 @@
 
  • 
   
   
@@ -128,7 +134,7 @@
 
    • 
 
 
-      
+
 
       
    
   
    
@@ -318,16 +324,16 @@ 
    Developers
    
 
 
    
   
    
-
    Site built with pkgdown 2.0.7.
    
+
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/news/index.html b/docs/news/index.html
index 83f22e7b5b..c9094f886d 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,9 +1,9 @@
 
-Changelog • scCustomizeChangelog • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -111,7 +117,110 @@ 
    Changelog 
    
     
    
 
     
    
-
    scCustomize 2.1.2 (2024-02-27)
    
+
    scCustomize 3.0.0 (2024-12-05)
    
+
    
+
    Added
    
+
    Major Updates to Functionality with rliger Package:
    Added new utility functions to interact with liger v2.0.0+ object format change:
    
+- Subset_LIGER to quickly subset by cluster or other meta data variable.
    
+- Cells_by_Identities_LIGER to extract list of barcodes sorted by values within given meta data column.
    
+
    Extended the following Seurat/SeuratObject generic functions to work seamlessly with liger objects:
    
+- Cells to extract vector of all cells or list vectors of cells by dataset.
    
+- Features to extract vector of all features or list vectors of features by dataset.
    
+- WhichCells to extract vector or list of cells matching identity criteria.
    
+- Embeddings to extract matrix containing dimensionality reduction embeddings or iNMF h.norm matrix.
    
+- Idents and Idents<- to extract and set default identities/clusters.
    
+
    Updated functions to interact with both old and new style liger objects:
    
+- plotFactors_scCustom()
    
+- Fetch_Meta
    
+- Top_Genes_Factor
    
+- Add_Mito_Ribo
    
+- Add_Cell_Complexity
    
+- DimPlot_LIGER
    
+- Variable_Features_ALL_LIGER
    
+- Feature_Present
    
+
    New functions compatible with old and new style liger objects:
    
+- Added new function Add_Hemo to add hemoglobin gene percentage for QC. Also added as parameter to Add_Cell_QC_Metrics. Add_Hemo supports all default species: (human, mouse, marmoset, zebrafish, rat, drosophila, rhesus macaque, and chicken) and works with both Seurat and liger objects.
    
+
    New scCustomize generics to function across both Seurat and Liger objects:
    
+- Add_Hemo (see above).
    
+- Rename_Clusters now S3 generic for setting new active.ident (Seurat) or defaultCluster (Liger).
    
+
    New functions for Seurat and rliger v2.0.0+ only: - Added new function Find_Factor_Cor to return correlation matrix between factor gene loadings from liger or Seurat object.
    
+- Added new function Factor_Cor_Plot to plot positive correlations from liger or Seurat object.
    
+
    Updated functions to recommend new rliger equivalents for users with rliger v2.0.0+:
    
+- as.LIGER
    
+- as.Seurat
    
+
    General scCustomize Updates:
    New functions:
    
+- Added new function Add_Hemo to add hemoglobin gene percentage for QC. Also added as parameter to Add_Cell_QC_Metrics. Add_Hemo supports all default species: (human, mouse, marmoset, zebrafish, rat, drosophila, and rhesus macaque) and works with both Seurat and liger objects.
    
+- Added new function seq_zeros() to create sequences with preceding zeros.
    
+- Added new function Read_Metrics_CellBender to read in the summary metrics csv file produced by CellBender. Can either read all metrics files from parent directory of output folders or a single metrics file.
    
+- Added Updated_MGI_Symbols to check for update gene names/symbols in mouse data (#202).
    
+- Added plotting function Proportion_Plot to plot pie chart or bar chart of proportion (or total counts) of cells in each identity class.
    
+- Added new function Random_Cells_Downsample to return either a vector or list with randomly downsampled cells for each identity class.
    
+- Added new function Cells_per_Sample to quickly return data.frame with just number of cells per sample.
    
+
    Updated functions:
    
+- Added new parameters data_name and overwrite to Add_Alt_Feature_ID to support new storage location.
    
+- Added cells parameter explicitly to FeatureScatter_scCustom.
    
+- Added Chicken (Gallus gallus) to default species for QC functions. Thanks @dpearton; (#176).
    
+- Added new plotting function SpatialDimPlot_scCustom. Thanks for encouragement @puapinyoying @nina-hahn (#160).
    
+- Added ability of Read_Metrics_10X to read a single metrics csv file and return data formatted the same way as when reading multiple files.
    
+- Added parameter cutoff_line_width to the QC_Plot_* family of plots to control line thickness of cutoff lines.
    
+- Cluster_Stats_All_Samples now returns data.frame with row order reflecting the frequency of cells.
    
+- Add_Mito_Ribo now supports datasets aligned to multi-species reference genomes (#184).
    
+- Added parameter add_prop_plot to DimPlot_scCustom to return plot showing number or percent of cells per identity along with the DimPlot.
    
+- Added optional parameter colors_use_assay2 to FeaturePlot_DualAssay which allows for specification of different palettes for the two plots (#182).
    
+- Added new folder and scripts (see “data-raw/” on GitHub) detailing the creation of gene lists used in Add_Cell_QC_Metrics.
    
+- Added ensembl ID support for percent hemoglobin, msigdb, and IEG gene sets (#186).
    
+- Add verbosity parameter to Store_Misc_Info_Seurat and Store_Palette_Seurat.
    
+- Explicitly reveal the reduction parameter in Cluster_Highlight_Plot and Meta_Highlight_Plot (#198).
    
+- Added show_row_names show_column_names, column_names_side, row_names_side, legend_position, legend_orientation, show_ident_legend, and show_ident_colors parameters to Clustered_DotPlot. Thanks for idea and code @johnminglu (#199).
    
+- Updated Split_Vector to allow user to specify number of chunks or size of chunks for splitting vector.
    
+- Update RenameClusters with additional parameters to enable storage of both old idents and new idents in meta.data within the function.
    
+- Update Add_Cell_QC_Metrics.Seurat to explicitly reveal list_species_names parameter.
    
+- Added new vignette for spatial plotting.
    
+- Added new and expanded vignette on use of object QC functions for better clarity on these functions and their uses (previously was part of QC Plotting & Helpers/Utilities Vignettes). Plotting elements of QC Plotting vignette are unchanged.
    
+
    
+
    
+
    Changed
    
+
    • 
+BREAKING CHANGES Add_Top_Gene_Pct_Seurat is now S3 generic that works with both Seurat and liger objects and has been renamed Add_Top_Gene_Pct.
      • 
+
    • 
+Add_Cell_QC_Metrics is now S3 generic and works with both Seurat and liger objects.
      • 
+
    • Changed storage location for Add_Alt_Feature_ID to @misc slot of object for safer storage across object filtering.
      • 
+
    • Added error check in as.anndata to explicitly check for installation of anndata before starting conversion (#162).
      • 
+
    • Updated Plot_Median_Genes, Plot_Median_UMIs, Plot_Median_Mito, Plot_Median_Other, Plot_Cells_per_Sample to understand “ident” as grouping variable.
      • 
+
    • Updated Store_Misc_Info_Seurat to use Seurat accessor/setter function Seurat::Misc().
      • 
+
    • Updated documentation for sample_names in Read_CellBender_h5_Multi_File to clarify parameter behavior (related to (#208)).
      • 
+
    • Updated Read_Metrics_10X to support adjusts to metrics summary format and metric names in output from Cell Ranger v9+.
      • 
+
    • Some reorganization of R/ directory/scripts.
      • 
+
    
+
    
+
    Fixes
    
+
    • Nebulosa plotting functions Plot_Density_Custom and Plot_Density_Joint_Only have been re-enabled for users with ggplot2 v3.5.0 following Nebulosa v1.12.1 update patch.
      • 
+
    • Fixed bug causing error in Add_Cell_QC_Metrics when overwrite = TRUE (#165).
      • 
+
    • Fixed wrong description of parameter in manual entry for DotPlot_scCustom (#158).
      • 
+
    • Fixed several potential errors in as.anndata from Seurat conversion that previously caused failures (#168).
      • 
+
    • Fixed errors in Create_Cluster_Annotation_File if for file path and csv name errors.
      • 
+
    • Fixed error when using plot_median and more than one feature in VlnPlot_scCustom (#169).
      • 
+
    • Fixed bug while collecting legends for DimPlot_scCustom due to changes in guides updated with ggplot2 v3.5.0 (#171).
      • 
+
    • Fixed error in Add_Sample_Meta that still errored when setting na_ok = TRUE.
      • 
+
    • Fixed errors in Plot_Median_* family that caused issues when group_by parameter was NULL.
      • 
+
    • Fixed errors in FeaturePlot_scCustom when setting combine = FALSE.
      • 
+
    • Fixed bug in DimPlot_scCustom that could cause blank plot when rasterizing points.
      • 
+
    • Fixed bug in MAD_Stats that didn’t respect mad_num parameter (#183).
      • 
+
    • Fixed bugs in MAD_Stats that could cause issues if mad_num was less than or equal to 0 and returned error if setting group_by_var to “ident”.
      • 
+
    • Replaced lingering instances of deprecated tidyr code .data[[“var”]] with update all_of/any_of syntax.
      • 
+
    • Fixed issue that could occur with some meta data modifying functions due to column name collisions in internals of function (#193).
      • 
+
    • Fixed issue that caused error when using Cluster_Highlight_Plot with split.by parameter (#201).
      • 
+
    • Added check and informative error message to Convert_Assay (#205).
      • 
+
    • Fixed issue with anndata conversion and Seurat V5 objects (#195).
      • 
+
    • Fixed issue with Updated_HGNC_Symbols due to change in URL path for gene names (#209).
      • 
+
    • Fixed bug in DimPlot_scCustom when split.by and label.box = TRUE.
      • 
+
    • Fixed bug in DiscretePalette_scCustom that didn’t error when supplying invalid palette names.
      • 
+
    • Fixed bug in DimPlot_LIGER that provided uniformative error message when changing the default cluster ident.
      • 
+
    • Spelling and style fixes. Thanks @kew24.
      • 
+
    
+
    
+    
    
+
    scCustomize 2.1.2 (2024-02-27)2024-02-28
    
 
    
 
    Added
    
 
    • None.
      • 
@@ -147,7 +256,7 @@ 
      AddedSeurat::LogSeuratCommand().
      
+
    • Added command logging to QC metric-related commands using Seurat::LogSeuratCommand().
      • 
 
    • Added parameter plot_legend to plotFactors_scCustom to allow for removal to legend in factor loading plots.
      • 
 
    • Added new functionality to Iterate_FeaturePlot_scCustom to allow for plotting multiple plots per page when saving to single PDF document (see new parameters: features_per_page and landscape.
      • 
 
    • Added LIGER_Features utility function for LIGER objects (analogous to Seurat::Features()).
      • 
@@ -438,7 +547,7 @@ 
      Added#60).
      
 
    • Added Add_Sample_Meta function for addition of sample-level meta data to cell-level @meta.data slot of Seurat objects.
      • 
-
    • Added a matrix check in Read_GEO_Delim to check for issues with imported matrices. Check is modified version of SeuratObject::CheckMatrix called CheckMatrix_scCustom(). Will warn if infinite, logical, non-integer (whole), or NA/NaN values are detected in input matrix.
      • 
+
    • Added a matrix check in Read_GEO_Delim to check for issues with imported matrices. Check is modified version of SeuratObject::CheckMatrix called CheckMatrix_scCustom(). Will warn if infinite, logical, non-integer (whole), or NA/NaN values are detected in input matrix.
      • 
 
    • 
 QC_Plot_UMIvsGene will now returned filtered correlation value that takes into account meta_gradient_name if provided in addition to nFeature_RNA and nCount_RNA.
      • 
 
    • Added new function Variable_Features_ALL_LIGER which allows for detection/selection of variable genes from entire LIGER object instead of iterating by dataset.
      • 
@@ -569,15 +678,15 @@ 
      Changes
-  
      Site built with pkgdown 2.0.7.
      
+  
      Site built with pkgdown 2.1.0.
      
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 084ef83a15..52153f2c14 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,25 +1,26 @@
-pandoc: 3.1.4
-pkgdown: 2.0.7
+pandoc: '3.2'
+pkgdown: 2.1.0
 pkgdown_sha: ~
 articles:
-  Cell_Bender_Functions: Cell_Bender_Functions.html
-  Color_Palettes: Color_Palettes.html
-  FAQ: FAQ.html
-  Gene_Expression_Plotting: Gene_Expression_Plotting.html
-  Helpers_and_Utilities: Helpers_and_Utilities.html
-  Installation: Installation.html
-  Iterative_Plotting: Iterative_Plotting.html
-  LIGER_Functions: LIGER_Functions.html
-  Markers_and_Cluster_Annotation: Markers_and_Cluster_Annotation.html
-  Misc_Functions: Misc_Functions.html
-  Object_Conversion: Object_Conversion.html
-  QC_Plots: QC_Plots.html
-  Read_and_Write_Functions: Read_and_Write_Functions.html
-  Sequencing_QC_Plots: Sequencing_QC_Plots.html
-  Statistics: Statistics.html
-  Update_Gene_Symbols: Update_Gene_Symbols.html
-last_built: 2024-02-28T19:49Z
+  articles/Cell_Bender_Functions: Cell_Bender_Functions.html
+  articles/Color_Palettes: Color_Palettes.html
+  articles/FAQ: FAQ.html
+  articles/Gene_Expression_Plotting: Gene_Expression_Plotting.html
+  articles/Helpers_and_Utilities: Helpers_and_Utilities.html
+  articles/Installation: Installation.html
+  articles/Iterative_Plotting: Iterative_Plotting.html
+  articles/LIGER_Functions: LIGER_Functions.html
+  articles/Markers_and_Cluster_Annotation: Markers_and_Cluster_Annotation.html
+  articles/Misc_Functions: Misc_Functions.html
+  articles/Object_Conversion: Object_Conversion.html
+  articles/Object_QC_Functions: Object_QC_Functions.html
+  articles/QC_Plots: QC_Plots.html
+  articles/Read_and_Write_Functions: Read_and_Write_Functions.html
+  articles/Sequencing_QC_Plots: Sequencing_QC_Plots.html
+  articles/Spatial_Plotting: Spatial_Plotting.html
+  articles/Statistics: Statistics.html
+  articles/Update_Gene_Symbols: Update_Gene_Symbols.html
+last_built: 2024-12-05T19:28Z
 urls:
   reference: https://samuel-marsh.github.io/scCustomize/reference
   article: https://samuel-marsh.github.io/scCustomize/articles
-
diff --git a/docs/reference/Add_Alt_Feature_ID.html b/docs/reference/Add_Alt_Feature_ID.html
index 5461f0b3bb..468835c803 100644
--- a/docs/reference/Add_Alt_Feature_ID.html
+++ b/docs/reference/Add_Alt_Feature_ID.html
@@ -1,9 +1,9 @@
 
-Add Alternative Feature IDs — Add_Alt_Feature_ID • scCustomizeAdd Alternative Feature IDs — Add_Alt_Feature_ID • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -112,7 +118,7 @@ 
    Add Alternative Feature IDs
    
     
    
 
     
    
-    
    Add alternative feature ids to the assay level meta.data slot in Assay5 compatible object (Seurat V5.0.0 or greater)
    
+    
    Add alternative feature ids data.frame to the misc slot of Seurat object.
    
     
    
 
     
    
@@ -120,41 +126,52 @@ 
    Add Alternative Feature IDs
    
   seurat_object,
   features_tsv_file = NULL,
   hdf5_file = NULL,
-  assay = NULL
+  assay = NULL,
+  data_name = "feature_id_mapping_table",
+  overwrite = FALSE
 )
    
     
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    object name.
    
 
 
-
    features_tsv_file
    
+
    features_tsv_file
    
 
    output file from Cell Ranger used for creation of Seurat object.
 (Either provide this of hdf5_file)
    
 
 
-
    hdf5_file
    
+
    hdf5_file
    
 
    output file from Cell Ranger used for creation of Seurat object.
 (Either provide this of features_tsv_file)
    
 
 
-
    assay
    
+
    assay
    
 
    name of assay(s) to add the alternative features to.  Can specify "all"
 to add to all assays.
    
 
+
+
    data_name
    
+
    name to use for data.frame when stored in @misc slot.
    
+
+
+
    overwrite
    
+
    logical, whether to overwrite item with the same data_name in the
+@misc slot of object (default is FALSE).
    
+
 
    
     
    
     
    Value
    
-    
-
-
    Seurat Object with new entries in the obj@assays$ASSAY@meta.data slot.
    
+    
    Seurat Object with new entries in the obj@misc slot.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # Using features.tsv.gz file
    # Either file from filtered or raw outputs can be used as they are identical.
 obj <- Add_Alt_Feature_ID(seurat_object = obj,
@@ -165,7 +182,7 @@ 
    Examples
    
    # Though it is faster to load filtered_feature_bc file due to droplet filtering
 obj <- Add_Alt_Feature_ID(seurat_object = obj,
 hdf5_file = "sample01/outs/outs/filtered_feature_bc_matrix.h5", assay = "RNA")
-}
+} # }
 
 
    
     
    
@@ -181,15 +198,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Add_CellBender_Diff.html b/docs/reference/Add_CellBender_Diff.html
index cecc414cfa..89a1838e7e 100644
--- a/docs/reference/Add_CellBender_Diff.html
+++ b/docs/reference/Add_CellBender_Diff.html
@@ -1,9 +1,9 @@
 
-Calculate and add differences post-cell bender analysis — Add_CellBender_Diff • scCustomizeCalculate and add differences post-cell bender analysis — Add_CellBender_Diff • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
     
    
     
    Calculate and add differences post-cell bender analysis
    
-    Source: R/Object_Utilities.R
+    Source: R/QC_Utilities_Seurat.R
     
     
    
 
@@ -121,31 +127,31 @@ 
    Calculate and add differences post-cell bender analysis
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    object name.
    
 
 
-
    raw_assay_name
    
+
    raw_assay_name
    
 
    name of the assay containing the raw data.
    
 
 
-
    cell_bender_assay_name
    
+
    cell_bender_assay_name
    
 
    name of the assay containing the Cell Bender'ed data.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Seurat object with 2 new columns in the meta.data slot.
    
+    
    Seurat object with 2 new columns in the meta.data slot.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 object <- Add_CellBender_Diff(seurat_object = obj, raw_assay_name = "RAW",
 cell_bender_assay_name = "RNA")
-}
+} # }
 
 
    
     
    
@@ -161,15 +167,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Add_Cell_Complexity.Seurat.html b/docs/reference/Add_Cell_Complexity.Seurat.html
new file mode 100644
index 0000000000..0ceefc298a
--- /dev/null
+++ b/docs/reference/Add_Cell_Complexity.Seurat.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Add_Cell_Complexity.html b/docs/reference/Add_Cell_Complexity.html
index 93166fa96f..7b729e9a48 100644
--- a/docs/reference/Add_Cell_Complexity.html
+++ b/docs/reference/Add_Cell_Complexity.html
@@ -1,9 +1,9 @@
 
-Add Cell Complexity — Add_Cell_Complexity • scCustomizeAdd Cell Complexity — Add_Cell_Complexity • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Add Cell Complexity
    
-    Source: R/Generics.R, R/LIGER_Utilities.R, R/Object_Utilities.R
+    Source: R/Generics.R, R/LIGER_Utilities.R, R/QC_Utilities_Seurat.R
     
     
    
 
@@ -118,7 +124,7 @@ 
    Add Cell Complexity
    
     
    
     
    Add_Cell_Complexity(object, ...)
 
-# S3 method for liger
+# S3 method for class 'liger'
 Add_Cell_Complexity(
   object,
   meta_col_name = "log10GenesPerUMI",
@@ -126,7 +132,7 @@ 
    Add Cell Complexity
    
   ...
 )
 
-# S3 method for Seurat
+# S3 method for class 'Seurat'
 Add_Cell_Complexity(
   object,
   meta_col_name = "log10GenesPerUMI",
@@ -138,41 +144,41 @@ 
    Add Cell Complexity
    
 
     
    
     
    Arguments
    
-    
    object
    
+
+
+
    object
    
 
    Seurat or LIGER object
    
 
 
-
    ...
    
+
    ...
    
 
    Arguments passed to other methods
    
 
 
-
    meta_col_name
    
+
    meta_col_name
    
 
    name to use for new meta data column.  Default is "log10GenesPerUMI".
    
 
 
-
    overwrite
    
+
    overwrite
    
 
    Logical.  Whether to overwrite existing an meta.data column.  Default is FALSE meaning that
 function will abort if column with name provided to meta_col_name is present in meta.data slot.
    
 
 
-
    assay
    
+
    assay
    
 
    assay to use in calculation.  Default is "RNA".  Note This should only be changed if
 storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).
    
 
 
    
     
    
     
    Value
    
-    
-
-
    An object of the same class as object with columns added to object meta data.
    
+    
    An object of the same class as object with columns added to object meta data.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # Liger
 liger_object <- Add_Cell_Complexity(object = liger_object)
-}
+} # }
 
 # Seurat
 library(Seurat)
@@ -192,15 +198,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Add_Cell_Complexity.liger.html b/docs/reference/Add_Cell_Complexity.liger.html
new file mode 100644
index 0000000000..0ceefc298a
--- /dev/null
+++ b/docs/reference/Add_Cell_Complexity.liger.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Add_Cell_Complexity_LIGER.html b/docs/reference/Add_Cell_Complexity_LIGER.html
index af0ebf9804..b67f8ba727 100644
--- a/docs/reference/Add_Cell_Complexity_LIGER.html
+++ b/docs/reference/Add_Cell_Complexity_LIGER.html
@@ -1,173 +1,8 @@
-
-Add Cell Complexity Value — Add_Cell_Complexity_LIGER • scCustomize
-    
-
-    
    
-      
    
-
-      
-
-      
    
-  
    
-    
    
-    
    Add Cell Complexity Value
    
-    Source: R/LIGER_Utilities.R
-    
-    
    
-
-    
    
-    
    Add measure of cell complexity/novelty (log10PerUMI) for data QC.
    
-    
    
-
-    
    
-    
    Add_Cell_Complexity_LIGER(
-  liger_object,
-  meta_col_name = "log10GenesPerUMI",
-  overwrite = FALSE
-)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    liger_object
    
-
    object name.
    
-
-
-
    meta_col_name
    
-
    name to use for new meta data column.  Default is "log10GenesPerUMI".
    
-
-
-
    overwrite
    
-
    Logical.  Whether to overwrite existing an meta.data column.  Default is FALSE meaning that
-function will abort if column with name provided to meta_col_name is present in meta.data slot.
    
-
-
    
-    
    
-    
    Value
    
-    
-
-
    A LIGER Object
    
-    
    
-
-    
    
-    
    Examples
    
-    
    if (FALSE) {
-object <- Add_Cell_Complexity_LIGER(liger_object = object)
-}
-
-
    
-    
    
-  
    
-  
-
    
-
-
-      
    
-  
    Developed by Samuel Marsh.
    
-
    
-
-
    
-  
    Site built with pkgdown 2.0.7.
    
-
    
-
-      
    
-
-  
-
-
-  
-
-  
+
+  
+    
+    
+    
+  
+
 
diff --git a/docs/reference/Add_Cell_Complexity_Seurat.html b/docs/reference/Add_Cell_Complexity_Seurat.html
index a9d926f001..b67f8ba727 100644
--- a/docs/reference/Add_Cell_Complexity_Seurat.html
+++ b/docs/reference/Add_Cell_Complexity_Seurat.html
@@ -1,178 +1,8 @@
-
-Add Cell Complexity Value — Add_Cell_Complexity_Seurat • scCustomize
-    
-
-    
    
-      
    
-
-      
-
-      
    
-  
    
-    
    
-    
    Add Cell Complexity Value
    
-    Source: R/Object_Utilities.R
-    
-    
    
-
-    
    
-    
    Add measure of cell complexity/novelty (log10PerUMI) for data QC.
    
-    
    
-
-    
    
-    
    Add_Cell_Complexity_Seurat(
-  seurat_object,
-  meta_col_name = "log10GenesPerUMI",
-  assay = "RNA",
-  overwrite = FALSE
-)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    seurat_object
    
-
    object name.
    
-
-
-
    meta_col_name
    
-
    name to use for new meta data column.  Default is "log10GenesPerUMI".
    
-
-
-
    assay
    
-
    assay to use in calculation.  Default is "RNA".  Note This should only be changed if
-storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).
    
-
-
-
    overwrite
    
-
    Logical.  Whether to overwrite existing an meta.data column.  Default is FALSE meaning that
-function will abort if column with name provided to meta_col_name is present in meta.data slot.
    
-
-
    
-    
    
-    
    Value
    
-    
-
-
    A Seurat Object
    
-    
    
-
-    
    
-    
    Examples
    
-    
    library(Seurat)
-pbmc_small <- Add_Cell_Complexity_Seurat(seurat_object = pbmc_small)
-
-
    
-    
    
-  
    
-  
-
    
-
-
-      
    
-  
    Developed by Samuel Marsh.
    
-
    
-
-
    
-  
    Site built with pkgdown 2.0.7.
    
-
    
-
-      
    
-
-  
-
-
-  
-
-  
+
+  
+    
+    
+    
+  
+
 
diff --git a/docs/reference/Add_Cell_QC_Metrics.Seurat.html b/docs/reference/Add_Cell_QC_Metrics.Seurat.html
new file mode 100644
index 0000000000..cf9b12afdd
--- /dev/null
+++ b/docs/reference/Add_Cell_QC_Metrics.Seurat.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Add_Cell_QC_Metrics.html b/docs/reference/Add_Cell_QC_Metrics.html
index 4da5ecbbea..d0df741f48 100644
--- a/docs/reference/Add_Cell_QC_Metrics.html
+++ b/docs/reference/Add_Cell_QC_Metrics.html
@@ -1,9 +1,10 @@
 
-Add Multiple Cell Quality Control Values with Single Function — Add_Cell_QC_Metrics • scCustomizeAdd Multiple Cell Quality Control Values with Single Function — Add_Cell_QC_Metrics • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
     
    
     
    Add Multiple Cell Quality Control Values with Single Function
    
-    Source: R/Object_Utilities.R
+    Source: R/Generics.R, R/LIGER_Utilities.R, R/QC_Utilities_Seurat.R
     
     
    
 
     
    
-    
    Add Mito/Ribo %, Cell Complexity (log10GenesPerUMI), Top Gene Percent with single function call
    
+    
    Add Mito/Ribo %, Cell Complexity (log10GenesPerUMI), Top Gene Percent with single
+function call to Seurat or liger objects.
    
     
    
 
     
    
-    
    Add_Cell_QC_Metrics(
-  seurat_object,
+    
    Add_Cell_QC_Metrics(object, ...)
+
+# S3 method for class 'liger'
+Add_Cell_QC_Metrics(
+  object,
   add_mito_ribo = TRUE,
   add_complexity = TRUE,
   add_top_pct = TRUE,
   add_MSigDB = TRUE,
   add_IEG = TRUE,
+  add_hemo = TRUE,
   add_cell_cycle = TRUE,
   species,
   mito_name = "percent_mito",
@@ -134,153 +146,227 @@ 
    Add Multiple Cell Quality Control Values with Single Function
    
   apop_name = "percent_apop",
   dna_repair_name = "percent_dna_repair",
   ieg_name = "percent_ieg",
+  hemo_name = "percent_hemo",
   mito_pattern = NULL,
   ribo_pattern = NULL,
+  hemo_pattern = NULL,
   mito_features = NULL,
   ribo_features = NULL,
+  hemo_features = NULL,
   ensembl_ids = FALSE,
   num_top_genes = 50,
   assay = NULL,
-  overwrite = FALSE
+  list_species_names = FALSE,
+  overwrite = FALSE,
+  ...
+)
+
+# S3 method for class 'Seurat'
+Add_Cell_QC_Metrics(
+  object,
+  species,
+  add_mito_ribo = TRUE,
+  add_complexity = TRUE,
+  add_top_pct = TRUE,
+  add_MSigDB = TRUE,
+  add_IEG = TRUE,
+  add_hemo = TRUE,
+  add_cell_cycle = TRUE,
+  mito_name = "percent_mito",
+  ribo_name = "percent_ribo",
+  mito_ribo_name = "percent_mito_ribo",
+  complexity_name = "log10GenesPerUMI",
+  top_pct_name = NULL,
+  oxphos_name = "percent_oxphos",
+  apop_name = "percent_apop",
+  dna_repair_name = "percent_dna_repair",
+  ieg_name = "percent_ieg",
+  hemo_name = "percent_hemo",
+  mito_pattern = NULL,
+  ribo_pattern = NULL,
+  hemo_pattern = NULL,
+  mito_features = NULL,
+  ribo_features = NULL,
+  hemo_features = NULL,
+  ensembl_ids = FALSE,
+  num_top_genes = 50,
+  assay = NULL,
+  list_species_names = FALSE,
+  overwrite = FALSE,
+  ...
 )
    
     
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
-
    object name.
    
 
 
-
    add_mito_ribo
    
+
    object
    
+
    Seurat or LIGER object
    
+
+
+
    ...
    
+
    Arguments passed to other methods
    
+
+
+
    add_mito_ribo
    
 
    logical, whether to add percentage of counts belonging to mitochondrial/ribosomal
 genes to object (Default is TRUE).
    
 
 
-
    add_complexity
    
+
    add_complexity
    
 
    logical, whether to add Cell Complexity to object (Default is TRUE).
    
 
 
-
    add_top_pct
    
+
    add_top_pct
    
 
    logical, whether to add Top Gene Percentages to object (Default is TRUE).
    
 
 
-
    add_MSigDB
    
+
    add_MSigDB
    
 
    logical, whether to add percentages of counts belonging to genes from of mSigDB hallmark
 gene lists: "HALLMARK_OXIDATIVE_PHOSPHORYLATION", "HALLMARK_APOPTOSIS", and "HALLMARK_DNA_REPAIR" to
 object (Default is TRUE).
    
 
 
-
    add_IEG
    
+
    add_IEG
    
 
    logical, whether to add percentage of counts belonging to IEG genes to object (Default is TRUE).
    
 
 
-
    add_cell_cycle
    
+
    add_hemo
    
+
    logical, whether to add percentage of counts belonging to homoglobin genes to object (Default is TRUE).
    
+
+
+
    add_cell_cycle
    
 
    logical, whether to addcell cycle scores and phase based on
 CellCycleScoring.  Only applicable if species = "human".  (Default is TRUE).
    
 
 
-
    species
    
+
    species
    
 
    Species of origin for given Seurat Object.  If mouse, human, marmoset, zebrafish, rat,
-drosophila, or rhesus macaque (name or abbreviation) are provided the function will automatically
-generate mito_pattern and ribo_pattern values.
    
+drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automatically
+generate patterns and features.
    
 
 
-
    mito_name
    
+
    mito_name
    
 
    name to use for the new meta.data column containing percent mitochondrial counts.
 Default is "percent_mito".
    
 
 
-
    ribo_name
    
+
    ribo_name
    
 
    name to use for the new meta.data column containing percent ribosomal counts.
 Default is "percent_ribo".
    
 
 
-
    mito_ribo_name
    
+
    mito_ribo_name
    
 
    name to use for the new meta.data column containing percent
 mitochondrial+ribosomal counts.  Default is "percent_mito_ribo".
    
 
 
-
    complexity_name
    
-
    name to use for new meta data column for Add_Cell_Complexity_Seurat.
+
    complexity_name
    
+
    name to use for new meta data column for Add_Cell_Complexity.
 Default is "log10GenesPerUMI".
    
 
 
-
    top_pct_name
    
-
    name to use for new meta data column for Add_Top_Gene_Pct_Seurat.
+
    top_pct_name
    
+
    name to use for new meta data column for Add_Top_Gene_Pct.
 Default is "percent_topXX", where XX is equal to the value provided to num_top_genes.
    
 
 
-
    oxphos_name
    
+
    oxphos_name
    
 
    name to use for new meta data column for percentage of MSigDB oxidative phosphorylation
 counts.  Default is "percent_oxphos".
    
 
 
-
    apop_name
    
+
    apop_name
    
 
    name to use for new meta data column for percentage of MSigDB apoptosis counts.
 Default is "percent_apop".
    
 
 
-
    dna_repair_name
    
+
    dna_repair_name
    
 
    name to use for new meta data column for percentage of MSigDB DNA repair
 counts.  Default is "percent_dna_repair"..
    
 
 
-
    ieg_name
    
+
    ieg_name
    
 
    name to use for new meta data column for percentage of IEG counts.  Default is "percent_ieg".
    
 
 
-
    mito_pattern
    
+
    hemo_name
    
+
    name to use for the new meta.data column containing percent hemoglobin counts.
+Default is "percent_mito".
    
+
+
+
    mito_pattern
    
 
    A regex pattern to match features against for mitochondrial genes (will set automatically if
 species is mouse or human; marmoset features list saved separately).
    
 
 
-
    ribo_pattern
    
+
    ribo_pattern
    
 
    A regex pattern to match features against for ribosomal genes
-(will set automatically if species is mouse, human, or marmoset).
    
+(will set automatically if species is in default list).
    
+
+
+
    hemo_pattern
    
+
    A regex pattern to match features against for hemoglobin genes
+(will set automatically if species is in default list).
    
 
 
-
    mito_features
    
+
    mito_features
    
 
    A list of mitochondrial gene names to be used instead of using regex pattern.
 Will override regex pattern if both are present (including default saved regex patterns).
    
 
 
-
    ribo_features
    
+
    ribo_features
    
 
    A list of ribosomal gene names to be used instead of using regex pattern.
 Will override regex pattern if both are present (including default saved regex patterns).
    
 
 
-
    ensembl_ids
    
+
    hemo_features
    
+
    A list of hemoglobin gene names to be used instead of using regex pattern.
+Will override regex pattern if both are present (including default saved regex patterns).
    
+
+
+
    ensembl_ids
    
 
    logical, whether feature names in the object are gene names or
 ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).
    
 
 
-
    num_top_genes
    
+
    num_top_genes
    
 
    An integer vector specifying the size(s) of the top set of high-abundance genes.
 Used to compute the percentage of library size occupied by the most highly expressed genes in each cell.
    
 
 
-
    assay
    
+
    assay
    
 
    assay to use in calculation.  Default is "RNA".  Note This should only be changed if
 storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).
    
 
 
-
    overwrite
    
+
    list_species_names
    
+
    returns list of all accepted values to use for default species names which
+contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, rhesus macaque, and
+chicken).  Default is FALSE.
    
+
+
+
    overwrite
    
 
    Logical.  Whether to overwrite existing an meta.data column.  Default is FALSE meaning that
 function will abort if column with name provided to meta_col_name is present in meta.data slot.
    
 
 
    
     
    
     
    Value
    
-    
-
+    
    A liger Object
    
 
    A Seurat Object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
-obj <- Add_Cell_QC_Metrics(seurat_object = obj, species = "Human")
-}
+    
    if (FALSE) { # \dontrun{
+obj <- Add_Cell_QC_Metrics(object = obj, species = "Human")
+} # }
+
+if (FALSE) { # \dontrun{
+obj <- Add_Cell_QC_Metrics(object = obj, species = "Human")
+} # }
 
 
    
     
    
@@ -296,15 +382,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Add_Cell_QC_Metrics.liger.html b/docs/reference/Add_Cell_QC_Metrics.liger.html
new file mode 100644
index 0000000000..cf9b12afdd
--- /dev/null
+++ b/docs/reference/Add_Cell_QC_Metrics.liger.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Add_Hemo.Seurat.html b/docs/reference/Add_Hemo.Seurat.html
new file mode 100644
index 0000000000..99293dc075
--- /dev/null
+++ b/docs/reference/Add_Hemo.Seurat.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Add_Hemo.html b/docs/reference/Add_Hemo.html
new file mode 100644
index 0000000000..c9d7279092
--- /dev/null
+++ b/docs/reference/Add_Hemo.html
@@ -0,0 +1,252 @@
+
+Add Hemoglobin percentages — Add_Hemo • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Add Hemoglobin percentages
    
+    Source: R/Generics.R, R/LIGER_Utilities.R, R/QC_Utilities_Seurat.R
+    
+    
    
+
+    
    
+    
    Add hemoglobin percentages to meta.data slot of Seurat Object or
+cell.data/cellMeta slot of Liger object
    
+    
    
+
+    
    
+    
    Add_Hemo(object, ...)
+
+# S3 method for class 'liger'
+Add_Hemo(
+  object,
+  species,
+  hemo_name = "percent_hemo",
+  hemo_pattern = NULL,
+  hemo_features = NULL,
+  ensembl_ids = FALSE,
+  overwrite = FALSE,
+  list_species_names = FALSE,
+  ...
+)
+
+# S3 method for class 'Seurat'
+Add_Hemo(
+  object,
+  species,
+  hemo_name = "percent_hemo",
+  hemo_pattern = NULL,
+  hemo_features = NULL,
+  ensembl_ids = FALSE,
+  assay = NULL,
+  overwrite = FALSE,
+  list_species_names = FALSE,
+  ...
+)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    object
    
+
    Seurat or LIGER object
    
+
+
+
    ...
    
+
    Arguments passed to other methods
    
+
+
+
    species
    
+
    Species of origin for given Seurat Object.  If mouse, human, marmoset, zebrafish, rat,
+drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automatically
+generate hemo_pattern values.
    
+
+
+
    hemo_name
    
+
    name to use for the new meta.data column containing percent hemoglobin counts.
+Default is "percent_hemo".
    
+
+
+
    hemo_pattern
    
+
    A regex pattern to match features against for hemoglobin genes (will set automatically if
+species is mouse or human; marmoset features list saved separately).
    
+
+
+
    hemo_features
    
+
    A list of hemoglobin gene names to be used instead of using regex pattern.
    
+
+
+
    ensembl_ids
    
+
    logical, whether feature names in the object are gene names or
+ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).
    
+
+
+
    overwrite
    
+
    Logical.  Whether to overwrite existing meta.data columns.  Default is FALSE meaning that
+function will abort if columns with any one of the names provided to hemo_name is
+present in meta.data slot.
    
+
+
+
    list_species_names
    
+
    returns list of all accepted values to use for default species names which
+contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, and
+rhesus macaque).  Default is FALSE.
    
+
+
+
    assay
    
+
    Assay to use (default is the current object default assay).
    
+
+
    
+    
    
+    
    Value
    
+    
    An object of the same class as object with columns added to object meta data.
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+# Liger
+liger_object <- Add_Hemo(object = liger_object, species = "human")
+} # }
+
+if (FALSE) { # \dontrun{
+# Seurat
+seurat_object <- Add_Hemo(object = seurat_object, species = "human")
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Add_Hemo.liger.html b/docs/reference/Add_Hemo.liger.html
new file mode 100644
index 0000000000..99293dc075
--- /dev/null
+++ b/docs/reference/Add_Hemo.liger.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Add_Mito_Ribo.Seurat.html b/docs/reference/Add_Mito_Ribo.Seurat.html
new file mode 100644
index 0000000000..aa3a55752a
--- /dev/null
+++ b/docs/reference/Add_Mito_Ribo.Seurat.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Add_Mito_Ribo.html b/docs/reference/Add_Mito_Ribo.html
index 224c2d6e53..0652f9f2c2 100644
--- a/docs/reference/Add_Mito_Ribo.html
+++ b/docs/reference/Add_Mito_Ribo.html
@@ -1,10 +1,10 @@
 
-Add Mito and Ribo percentages — Add_Mito_Ribo • scCustomizeAdd Mito and Ribo percentages — Add_Mito_Ribo • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
     
    
     
    Add Mito and Ribo percentages
    
-    Source: R/Generics.R, R/LIGER_Utilities.R, R/Object_Utilities.R
+    Source: R/Generics.R, R/LIGER_Utilities.R, R/QC_Utilities_Seurat.R
     
     
    
 
@@ -120,7 +126,7 @@ 
    Add Mito and Ribo percentages
    
     
    
     
    Add_Mito_Ribo(object, ...)
 
-# S3 method for liger
+# S3 method for class 'liger'
 Add_Mito_Ribo(
   object,
   species,
@@ -137,7 +143,7 @@ 
    Add Mito and Ribo percentages
    
   ...
 )
 
-# S3 method for Seurat
+# S3 method for class 'Seurat'
 Add_Mito_Ribo(
   object,
   species,
@@ -152,100 +158,108 @@ 
    Add Mito and Ribo percentages
    
   assay = NULL,
   overwrite = FALSE,
   list_species_names = FALSE,
+  species_prefix = NULL,
   ...
 )
    
     
    
 
     
    
     
    Arguments
    
-    
    object
    
+
+
+
    object
    
 
    Seurat or LIGER object
    
 
 
-
    ...
    
+
    ...
    
 
    Arguments passed to other methods
    
 
 
-
    species
    
+
    species
    
 
    Species of origin for given Seurat Object.  If mouse, human, marmoset, zebrafish, rat,
-drosophila, or rhesus macaque (name or abbreviation) are provided the function will automatically
+drosophila, rhesus macaque, or chicken (name or abbreviation) are provided the function will automatically
 generate mito_pattern and ribo_pattern values.
    
 
 
-
    mito_name
    
+
    mito_name
    
 
    name to use for the new meta.data column containing percent mitochondrial counts.
 Default is "percent_mito".
    
 
 
-
    ribo_name
    
+
    ribo_name
    
 
    name to use for the new meta.data column containing percent ribosomal counts.
 Default is "percent_ribo".
    
 
 
-
    mito_ribo_name
    
+
    mito_ribo_name
    
 
    name to use for the new meta.data column containing percent
 mitochondrial+ribosomal counts.  Default is "percent_mito_ribo".
    
 
 
-
    mito_pattern
    
+
    mito_pattern
    
 
    A regex pattern to match features against for mitochondrial genes (will set automatically if
-species is mouse or human; marmoset features list saved separately).
    
+species is mouse, human, zebrafish, rat, drosophila, rhesus macaque, or chicken;
+marmoset features list saved separately).
    
 
 
-
    ribo_pattern
    
+
    ribo_pattern
    
 
    A regex pattern to match features against for ribosomal genes
-(will set automatically if species is mouse, human, or marmoset).
    
+(will set automatically if species is mouse, human, marmoset, zebrafish, rat,
+drosophila, rhesus macaque, or chicken).
    
 
 
-
    mito_features
    
+
    mito_features
    
 
    A list of mitochondrial gene names to be used instead of using regex pattern.
 Will override regex pattern if both are present (including default saved regex patterns).
    
 
 
-
    ribo_features
    
+
    ribo_features
    
 
    A list of ribosomal gene names to be used instead of using regex pattern.
 Will override regex pattern if both are present (including default saved regex patterns).
    
 
 
-
    ensembl_ids
    
+
    ensembl_ids
    
 
    logical, whether feature names in the object are gene names or
 ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).
    
 
 
-
    overwrite
    
+
    overwrite
    
 
    Logical.  Whether to overwrite existing meta.data columns.  Default is FALSE meaning that
 function will abort if columns with any one of the names provided to mito_name ribo_name or
 mito_ribo_name is present in meta.data slot.
    
 
 
-
    list_species_names
    
+
    list_species_names
    
 
    returns list of all accepted values to use for default species names which
-contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, and
-rhesus macaque).  Default is FALSE.
    
+contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, rhesus macaque, and
+chicken).  Default is FALSE.
    
 
 
-
    assay
    
+
    assay
    
 
    Assay to use (default is the current object default assay).
    
 
+
+
    species_prefix
    
+
    the species prefix in front of gene symbols in object if providing two species for
+multi-species aligned dataset.
    
+
 
    
     
    
     
    Value
    
-    
-
-
    An object of the same class as object with columns added to object meta data.
    
+    
    An object of the same class as object with columns added to object meta data.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # Liger
 liger_object <- Add_Mito_Ribo(object = liger_object, species = "human")
-}
+} # }
 
-if (FALSE) {
+if (FALSE) { # \dontrun{
 # Seurat
 seurat_object <- Add_Mito_Ribo(object = seurat_object, species = "human")
-}
+} # }
 
 
    
     
    
@@ -261,15 +275,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Add_Mito_Ribo.liger.html b/docs/reference/Add_Mito_Ribo.liger.html
new file mode 100644
index 0000000000..aa3a55752a
--- /dev/null
+++ b/docs/reference/Add_Mito_Ribo.liger.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Add_Mito_Ribo_LIGER.html b/docs/reference/Add_Mito_Ribo_LIGER.html
index 4f06f50869..b67f8ba727 100644
--- a/docs/reference/Add_Mito_Ribo_LIGER.html
+++ b/docs/reference/Add_Mito_Ribo_LIGER.html
@@ -1,231 +1,8 @@
-
-Add Mito and Ribo percentages to LIGER — Add_Mito_Ribo_LIGER • scCustomize
-    
-
-    
    
-      
    
-
-      
-
-      
    
-  
    
-    
    
-    
    Add Mito and Ribo percentages to LIGER
    
-    Source: R/LIGER_Utilities.R
-    
-    
    
-
-    
    
-    
    Add Mito, Ribo, percentages to meta.data slot of LIGER Object
    
-    
    
-
-    
    
-    
    Add_Mito_Ribo_LIGER(
-  liger_object,
-  species,
-  mito_name = "percent_mito",
-  ribo_name = "percent_ribo",
-  mito_ribo_name = "percent_mito_ribo",
-  mito_pattern = NULL,
-  ribo_pattern = NULL,
-  mito_features = NULL,
-  ribo_features = NULL,
-  ensembl_ids = FALSE,
-  overwrite = FALSE,
-  list_species_names = FALSE
-)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    liger_object
    
-
    LIGER object name.
    
-
-
-
    species
    
-
    Species of origin for given Seurat Object.  If mouse, human, marmoset, zebrafish, rat,
-drosophila, or rhesus macaque (name or abbreviation) are provided the function will automatically
-generate mito_pattern and ribo_pattern values.
    
-
-
-
    mito_name
    
-
    name to use for the new meta.data column containing percent mitochondrial counts.
-Default is "percent_mito".
    
-
-
-
    ribo_name
    
-
    name to use for the new meta.data column containing percent ribosomal counts.
-Default is "percent_ribo".
    
-
-
-
    mito_ribo_name
    
-
    name to use for the new meta.data column containing percent mitochondrial+ribosomal
-counts.  Default is "percent_mito_ribo".
    
-
-
-
    mito_pattern
    
-
    A regex pattern to match features against for mitochondrial genes (will set automatically
-if species is mouse or human; marmoset features list saved separately).
    
-
-
-
    ribo_pattern
    
-
    A regex pattern to match features against for ribosomal genes (will set automatically
-if species is mouse, human, or marmoset).
    
-
-
-
    mito_features
    
-
    A list of mitochondrial gene names to be used instead of using regex pattern.
-Will override regex pattern if both are present (including default saved regex patterns).
    
-
-
-
    ribo_features
    
-
    A list of ribosomal gene names to be used instead of using regex pattern.
-Will override regex pattern if both are present (including default saved regex patterns).
    
-
-
-
    ensembl_ids
    
-
    logical, whether feature names in the object are gene names or
-ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).
    
-
-
-
    overwrite
    
-
    Logical.  Whether to overwrite existing meta.data columns.  Default is FALSE meaning that
-function will abort if columns with any one of the names provided to mito_name ribo_name or mito_ribo_name
-is present in meta.data slot.
    
-
-
-
    list_species_names
    
-
    returns list of all accepted values to use for default species names which
-contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, and
-rhesus macaque).  Default is FALSE.
    
-
-
    
-    
    
-    
    Value
    
-    
-
-
    A LIGER Object
    
-    
    
-
-    
    
-    
    Examples
    
-    
    if (FALSE) {
-object <- Add_Mito_Ribo_LIGER(liger_object = object, species = "mouse")
-}
-
-
    
-    
    
-  
    
-  
-
    
-
-
-      
    
-  
    Developed by Samuel Marsh.
    
-
    
-
-
    
-  
    Site built with pkgdown 2.0.7.
    
-
    
-
-      
    
-
-  
-
-
-  
-
-  
+
+  
+    
+    
+    
+  
+
 
diff --git a/docs/reference/Add_Mito_Ribo_Seurat.html b/docs/reference/Add_Mito_Ribo_Seurat.html
index 4ade446805..b67f8ba727 100644
--- a/docs/reference/Add_Mito_Ribo_Seurat.html
+++ b/docs/reference/Add_Mito_Ribo_Seurat.html
@@ -1,236 +1,8 @@
-
-Add Mito and Ribo percentages — Add_Mito_Ribo_Seurat • scCustomize
-    
-
-    
    
-      
    
-
-      
-
-      
    
-  
    
-    
    
-    
    Add Mito and Ribo percentages
    
-    Source: R/Object_Utilities.R
-    
-    
    
-
-    
    
-    
    Add Mito, Ribo, & Mito+Ribo percentages to meta.data slot of Seurat Object
    
-    
    
-
-    
    
-    
    Add_Mito_Ribo_Seurat(
-  seurat_object,
-  species,
-  mito_name = "percent_mito",
-  ribo_name = "percent_ribo",
-  mito_ribo_name = "percent_mito_ribo",
-  mito_pattern = NULL,
-  ribo_pattern = NULL,
-  mito_features = NULL,
-  ribo_features = NULL,
-  ensembl_ids = FALSE,
-  assay = NULL,
-  overwrite = FALSE,
-  list_species_names = FALSE
-)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    seurat_object
    
-
    object name.
    
-
-
-
    species
    
-
    Species of origin for given Seurat Object.  If mouse, human, marmoset, zebrafish, rat,
-drosophila, or rhesus macaque (name or abbreviation) are provided the function will automatically
-generate mito_pattern and ribo_pattern values.
    
-
-
-
    mito_name
    
-
    name to use for the new meta.data column containing percent mitochondrial counts.
-Default is "percent_mito".
    
-
-
-
    ribo_name
    
-
    name to use for the new meta.data column containing percent ribosomal counts.
-Default is "percent_ribo".
    
-
-
-
    mito_ribo_name
    
-
    name to use for the new meta.data column containing percent
-mitochondrial+ribosomal counts.  Default is "percent_mito_ribo".
    
-
-
-
    mito_pattern
    
-
    A regex pattern to match features against for mitochondrial genes (will set automatically if
-species is mouse or human; marmoset features list saved separately).
    
-
-
-
    ribo_pattern
    
-
    A regex pattern to match features against for ribosomal genes
-(will set automatically if species is mouse, human, or marmoset).
    
-
-
-
    mito_features
    
-
    A list of mitochondrial gene names to be used instead of using regex pattern.
-Will override regex pattern if both are present (including default saved regex patterns).
    
-
-
-
    ribo_features
    
-
    A list of ribosomal gene names to be used instead of using regex pattern.
-Will override regex pattern if both are present (including default saved regex patterns).
    
-
-
-
    ensembl_ids
    
-
    logical, whether feature names in the object are gene names or
-ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).
    
-
-
-
    assay
    
-
    Assay to use (default is the current object default assay).
    
-
-
-
    overwrite
    
-
    Logical.  Whether to overwrite existing meta.data columns.  Default is FALSE meaning that
-function will abort if columns with any one of the names provided to mito_name ribo_name or
-mito_ribo_name is present in meta.data slot.
    
-
-
-
    list_species_names
    
-
    returns list of all accepted values to use for default species names which
-contain internal regex/feature lists (human, mouse, marmoset, zebrafish, rat, drosophila, and
-rhesus macaque).  Default is FALSE.
    
-
-
    
-    
    
-    
    Value
    
-    
-
-
    A Seurat Object
    
-    
    
-
-    
    
-    
    Examples
    
-    
    if (FALSE) {
-obj <- Add_Mito_Ribo_Seurat(seurat_object = obj, species = "human")
-}
-
-
    
-    
    
-  
    
-  
-
    
-
-
-      
    
-  
    Developed by Samuel Marsh.
    
-
    
-
-
    
-  
    Site built with pkgdown 2.0.7.
    
-
    
-
-      
    
-
-  
-
-
-  
-
-  
+
+  
+    
+    
+    
+  
+
 
diff --git a/docs/reference/Add_Pct_Diff.html b/docs/reference/Add_Pct_Diff.html
index 55fd6f9c55..9c1ae5b4f2 100644
--- a/docs/reference/Add_Pct_Diff.html
+++ b/docs/reference/Add_Pct_Diff.html
@@ -1,9 +1,9 @@
 
-Add percentage difference to DE results — Add_Pct_Diff • scCustomizeAdd percentage difference to DE results — Add_Pct_Diff • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -126,41 +132,41 @@ 
    Add percentage difference to DE results
    
 
     
    
     
    Arguments
    
-    
    marker_dataframe
    
+
+
+
    marker_dataframe
    
 
    data.frame containing the results of FindMarkers,  FindAllMarkers, or other DE test data.frame.
    
 
 
-
    pct.1_name
    
+
    pct.1_name
    
 
    the name of data.frame column corresponding to percent expressed in group 1.
 Default is Seurat default "pct.1".
    
 
 
-
    pct.2_name
    
+
    pct.2_name
    
 
    the name of data.frame column corresponding to percent expressed in group 2.
 Default is Seurat default "pct.2".
    
 
 
-
    overwrite
    
+
    overwrite
    
 
    logical.  If the marker_dataframe already contains column named "pct_diff" whether to
 overwrite or return error message.  Default is FALSE.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Returns input marker_dataframe with additional "pct_diff" column.
    
+    
    Returns input marker_dataframe with additional "pct_diff" column.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 marker_df <- FindAllMarkers(object = obj_name)
 marker_df <- Add_Pct_Diff(marker_dataframe = marker_df)
 # or piped with function
 marker_df <- FindAllMarkers(object = obj_name) %>%
   Add_Pct_Diff()
-}
+} # }
 
 
    
     
    
@@ -176,15 +182,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Add_Sample_Meta.html b/docs/reference/Add_Sample_Meta.html
index 337573deea..f506e83d5e 100644
--- a/docs/reference/Add_Sample_Meta.html
+++ b/docs/reference/Add_Sample_Meta.html
@@ -1,9 +1,9 @@
 
-Add Sample Level Meta Data — Add_Sample_Meta • scCustomizeAdd Sample Level Meta Data — Add_Sample_Meta • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -128,32 +134,34 @@ 
    Add Sample Level Meta Data
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    object name.
    
 
 
-
    meta_data
    
+
    meta_data
    
 
    data.frame/tibble containing meta data or path to file to read.  Must be formatted as
 either data.frame or tibble.
    
 
 
-
    join_by_seurat
    
+
    join_by_seurat
    
 
    name of the column in seurat_object@meta.data that contains matching
 variables to join_by_meta in meta_data.
    
 
 
-
    join_by_meta
    
+
    join_by_meta
    
 
    name of the column in meta_data that contains matching
 variables to join_by_seurat in seurat_object@meta.data.
    
 
 
-
    na_ok
    
+
    na_ok
    
 
    logical, is it ok to add NA values to seurat_object@meta.data.  Default is FALSE.
 Be very careful if setting TRUE because if there is error in join operation it may result in all
 @meta.data values being replaced with NA.
    
 
 
-
    overwrite
    
+
    overwrite
    
 
    logical, if there are shared columns between seurat_object@meta.data and meta_data
 should the current seurat_object@meta.data columns be overwritten.  Default is FALSE.  This parameter
 excludes values provided to join_by_seurat and join_by_meta.
    
@@ -161,14 +169,12 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    Seurat object with new @meta.data columns
    
+    
    Seurat object with new @meta.data columns
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # meta_data present in environment
 sample_level_meta <- data.frame(...)
 obj <- Add_Sample_Meta(seurat_object = obj, meta_data = sample_level_meta,
@@ -177,7 +183,7 @@ 
    Examples
    
 # from meta data file
 obj <- Add_Sample_Meta(seurat_object = obj, meta_data = "meta_data/sample_level_meta.csv",
 join_by_seurat = "orig.ident", join_by_meta = "sample_ID")
-}
+} # }
 
 
    
     
    
@@ -193,15 +199,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Add_Top_Gene_Pct.Seurat.html b/docs/reference/Add_Top_Gene_Pct.Seurat.html
new file mode 100644
index 0000000000..6bf02d39db
--- /dev/null
+++ b/docs/reference/Add_Top_Gene_Pct.Seurat.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Add_Top_Gene_Pct.html b/docs/reference/Add_Top_Gene_Pct.html
new file mode 100644
index 0000000000..7e7bb84cc5
--- /dev/null
+++ b/docs/reference/Add_Top_Gene_Pct.html
@@ -0,0 +1,240 @@
+
+Add Percent of High Abundance Genes — Add_Top_Gene_Pct • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Add Percent of High Abundance Genes
    
+    Source: R/Generics.R, R/LIGER_Utilities.R, R/QC_Utilities_Seurat.R
+    
+    
    
+
+    
    
+    
    Add the percentage of counts occupied by the top XX most highly expressed genes in each cell.
    
+    
    
+
+    
    
+    
    Add_Top_Gene_Pct(object, ...)
+
+# S3 method for class 'liger'
+Add_Top_Gene_Pct(
+  object,
+  num_top_genes = 50,
+  meta_col_name = NULL,
+  overwrite = FALSE,
+  verbose = TRUE,
+  ...
+)
+
+# S3 method for class 'Seurat'
+Add_Top_Gene_Pct(
+  object,
+  num_top_genes = 50,
+  meta_col_name = NULL,
+  assay = "RNA",
+  overwrite = FALSE,
+  verbose = TRUE,
+  ...
+)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    object
    
+
    Seurat or LIGER object.
    
+
+
+
    ...
    
+
    Arguments passed to other methods
    
+
+
+
    num_top_genes
    
+
    An integer vector specifying the size(s) of the top set of high-abundance genes.
+Used to compute the percentage of library size occupied by the most highly expressed genes in each cell.
    
+
+
+
    meta_col_name
    
+
    name to use for new meta data column.  Default is "percent_topXX", where XX is
+equal to the value provided to num_top_genes.
    
+
+
+
    overwrite
    
+
    Logical.  Whether to overwrite existing an meta.data column.  Default is FALSE meaning that
+function will abort if column with name provided to meta_col_name is present in meta.data slot.
    
+
+
+
    verbose
    
+
    logical, whether to print messages with status updates, default is TRUE.
    
+
+
+
    assay
    
+
    assay to use in calculation.  Default is "RNA".  Note This should only be changed if
+storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).
    
+
+
    
+    
    
+    
    Value
    
+    
    A liger Object
    
+
    A Seurat Object
    
+    
    
+    
    
+    
    References
    
+    
    This function uses scuttle package (license: GPL-3) to calculate the percent of expression
+coming from top XX genes in each cell.  Parameter description for num_top_genes also from scuttle.
+If using this function in analysis, in addition to citing scCustomize, please cite scuttle:
+McCarthy DJ, Campbell KR, Lun ATL, Willis QF (2017). “Scater: pre-processing, quality control,
+normalisation and visualisation of single-cell RNA-seq data in R.” Bioinformatics, 33, 1179-1186.
+doi:10.1093/bioinformatics/btw777.
    
+    
    
+    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+liger_object <- Add_Top_Gene_Pct(object = liger_object, num_top_genes = 50)
+} # }
+
+if (FALSE) { # \dontrun{
+library(Seurat)
+pbmc_small <- Add_Top_Gene_Pct(seurat_object = pbmc_small, num_top_genes = 50)
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Add_Top_Gene_Pct.liger.html b/docs/reference/Add_Top_Gene_Pct.liger.html
new file mode 100644
index 0000000000..6bf02d39db
--- /dev/null
+++ b/docs/reference/Add_Top_Gene_Pct.liger.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Add_Top_Gene_Pct_Seurat.html b/docs/reference/Add_Top_Gene_Pct_Seurat.html
index b675c1d3ab..b67f8ba727 100644
--- a/docs/reference/Add_Top_Gene_Pct_Seurat.html
+++ b/docs/reference/Add_Top_Gene_Pct_Seurat.html
@@ -1,211 +1,8 @@
-
-Add Percent of High Abundance Genes — Add_Top_Gene_Pct_Seurat • scCustomize
-    
-
-    
    
-      
    
-
-      
-
-      
    
-  
    
-    
    
-    
    Add Percent of High Abundance Genes
    
-    Source: R/Object_Utilities.R
-    
-    
    
-
-    
    
-    
    Add the percentage of counts occupied by the top XX most highly expressed genes in each cell.
    
-    
    
-
-    
    
-    
    Add_Top_Gene_Pct_Seurat(
-  seurat_object,
-  num_top_genes = 50,
-  meta_col_name = NULL,
-  assay = "RNA",
-  overwrite = FALSE,
-  verbose = TRUE
-)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    seurat_object
    
-
    object name.
    
-
-
-
    num_top_genes
    
-
    An integer vector specifying the size(s) of the top set of high-abundance genes.
-Used to compute the percentage of library size occupied by the most highly expressed genes in each cell.
    
-
-
-
    meta_col_name
    
-
    name to use for new meta data column.  Default is "percent_topXX", where XX is
-equal to the value provided to num_top_genes.
    
-
-
-
    assay
    
-
    assay to use in calculation.  Default is "RNA".  Note This should only be changed if
-storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).
    
-
-
-
    overwrite
    
-
    Logical.  Whether to overwrite existing an meta.data column.  Default is FALSE meaning that
-function will abort if column with name provided to meta_col_name is present in meta.data slot.
    
-
-
-
    verbose
    
-
    logical, whether to print messages with status updates, default is TRUE.
    
-
-
    
-    
    
-    
    Value
    
-    
-
-
    A Seurat Object
    
-    
    
-    
    
-    
    References
    
-    
    This function uses scuttle package (license: GPL-3) to calculate the percent of expression
-coming from top XX genes in each cell.  Parameter description for num_top_genes also from scuttle.
-If using this function in analysis, in addition to citing scCustomize, please cite scuttle:
-McCarthy DJ, Campbell KR, Lun ATL, Willis QF (2017). “Scater: pre-processing, quality control,
-normalisation and visualisation of single-cell RNA-seq data in R.” Bioinformatics, 33, 1179-1186.
-doi:10.1093/bioinformatics/btw777.
    
-    
    
-    
-
-    
    
-    
    Examples
    
-    
    if (FALSE) {
-library(Seurat)
-pbmc_small <- Add_Top_Gene_Pct_Seurat(seurat_object = pbmc_small, num_top_genes = 50)
-}
-
-
    
-    
    
-  
    
-  
-
    
-
-
-      
    
-  
    Developed by Samuel Marsh.
    
-
    
-
-
    
-  
    Site built with pkgdown 2.0.7.
    
-
    
-
-      
    
-
-  
-
-
-  
-
-  
+
+  
+    
+    
+    
+  
+
 
diff --git a/docs/reference/Barcode_Plot.html b/docs/reference/Barcode_Plot.html
index fd53fd3344..9f4fb3ccf6 100644
--- a/docs/reference/Barcode_Plot.html
+++ b/docs/reference/Barcode_Plot.html
@@ -1,9 +1,9 @@
 
-Create Barcode Rank Plot — Barcode_Plot • scCustomizeCreate Barcode Rank Plot — Barcode_Plot • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
     
    
     
    Create Barcode Rank Plot
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -127,44 +133,44 @@ 
    Create Barcode Rank Plot
    
 
     
    
     
    Arguments
    
-    
    br_out
    
+
+
+
    br_out
    
 
    DFrame output from barcodeRanks.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    point size for plotting, default is 6.
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Title for plot, default is "Barcode Ranks".
    
 
 
-
    raster_dpi
    
+
    raster_dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(1024, 1024).
    
 
 
-
    plateau
    
+
    plateau
    
 
    numerical value at which to add vertical line designating estimated
 empty droplet plateau (default is NULL).
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 mat <- Read10X_h5(filename = "raw_feature_bc_matrix.h5")
 
 br_results <- DropletUtils::barcodeRanks(mat)
 
 Barcode_Plot(br_out = br_results)
-}
+} # }
 
 
    
     
    
@@ -180,15 +186,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Blank_Theme-1.png b/docs/reference/Blank_Theme-1.png
index 7901ae927c..b6dcb95b9a 100644
Binary files a/docs/reference/Blank_Theme-1.png and b/docs/reference/Blank_Theme-1.png differ
diff --git a/docs/reference/Blank_Theme.html b/docs/reference/Blank_Theme.html
index 74397e5d16..4cc070e604 100644
--- a/docs/reference/Blank_Theme.html
+++ b/docs/reference/Blank_Theme.html
@@ -1,9 +1,9 @@
 
-Blank Theme — Blank_Theme • scCustomizeBlank Theme — Blank_Theme • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,15 +127,15 @@ 
    Blank Theme
    
 
     
    
     
    Arguments
    
-    
    ...
    
+
+
+
    ...
    
 
    extra arguments passed to ggplot2::theme().
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Returns a list-like object of class theme.
    
+    
    Returns a list-like object of class theme.
    
     
    
 
     
    
@@ -155,15 +161,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Case_Check.html b/docs/reference/Case_Check.html
index d72ddcb92a..3d17166ad1 100644
--- a/docs/reference/Case_Check.html
+++ b/docs/reference/Case_Check.html
@@ -1,12 +1,9 @@
 
-Check for alternate case features
-Checks Seurat object for the presence of features with the same spelling but alternate case. — Case_Check • scCustomizeCheck for alternate case features — Case_Check • scCustomize
-    
+
 
     
    
       
    
 
@@ -34,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
-    
    Check for alternate case features
-Checks Seurat object for the presence of features with the same spelling but alternate case.
    
+    
    Check for alternate case features
    
     Source: R/Utilities.R
     
     
    
 
     
    
-    
    Check for alternate case features
-Checks Seurat object for the presence of features with the same spelling but alternate case.
    
+    
    Checks Seurat object for the presence of features with the same spelling but alternate case.
    
     
    
 
     
    
@@ -132,40 +133,40 @@ 
    Check for alternate case features
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    gene_list
    
+
    gene_list
    
 
    vector of genes to check.
    
 
 
-
    case_check_msg
    
+
    case_check_msg
    
 
    logical. Whether to print message to console if alternate case features are
 found in addition to inclusion in returned list.  Default is TRUE.
    
 
 
-
    return_features
    
+
    return_features
    
 
    logical. Whether to return vector of alternate case features.  Default is TRUE.
    
 
 
-
    assay
    
+
    assay
    
 
    Name of assay to pull feature names from. If NULL will use the result of DefaultAssay(seurat_object).
    
 
 
    
     
    
     
    Value
    
-    
-
-
    If features found returns vector of found alternate case features and prints message depending on
+    
    If features found returns vector of found alternate case features and prints message depending on
 parameters specified.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 alt_features <- Case_Check(seurat_object = obj_name, gene_list = DEG_list)
-}
+} # }
 
 
    
     
    
@@ -181,15 +182,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/CellBender_Diff_Plot.html b/docs/reference/CellBender_Diff_Plot.html
index 2d49dd5365..76af78c05c 100644
--- a/docs/reference/CellBender_Diff_Plot.html
+++ b/docs/reference/CellBender_Diff_Plot.html
@@ -1,9 +1,9 @@
 
-Plot Number of Cells/Nuclei per Sample — CellBender_Diff_Plot • scCustomizePlot Number of Cells/Nuclei per Sample — CellBender_Diff_Plot • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
     
    
     
    Plot Number of Cells/Nuclei per Sample
    
-    Source: R/Statistics_Plotting.R
+    Source: R/Plotting_Statistics.R
     
     
    
 
@@ -143,115 +149,115 @@ 
    Plot Number of Cells/Nuclei per Sample
    
 
     
    
     
    Arguments
    
-    
    feature_diff_df
    
+
+
+
    feature_diff_df
    
 
    name of data.frame created using CellBender_Feature_Diff.
    
 
 
-
    pct_diff_threshold
    
+
    pct_diff_threshold
    
 
    threshold to use for feature plotting.  Resulting plot will only contain
 features which exhibit percent change >= value.  Default is 25.
    
 
 
-
    num_features
    
+
    num_features
    
 
    Number of features to plot.  Will ignore pct_diff_threshold and return
 plot with specified number of features.  Default is NULL.
    
 
 
-
    label
    
+
    label
    
 
    logical, whether or not to label the features that have largest percent difference
 between raw and CellBender counts (Default is TRUE).
    
 
 
-
    num_labels
    
+
    num_labels
    
 
    Number of features to label if label = TRUE, (default is 20).
    
 
 
-
    min_count_label
    
+
    min_count_label
    
 
    Minimum number of raw counts per feature necessary to be included in
 plot labels (default is 1)
    
 
 
-
    repel
    
+
    repel
    
 
    logical, whether to use geom_text_repel to create a nicely-repelled labels; this is
 slow when a lot of points are being plotted. If using repel, set xnudge and ynudge to 0, (Default is TRUE).
    
 
 
-
    custom_labels
    
+
    custom_labels
    
 
    A custom set of features to label instead of the features most different between
 raw and CellBender counts.
    
 
 
-
    plot_line
    
+
    plot_line
    
 
    logical, whether to plot diagonal line with slope = 1 (Default is TRUE).
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Plot title.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    xnudge
    
+
    xnudge
    
 
    Amount to nudge X and Y coordinates of labels by.
    
 
 
-
    ynudge
    
+
    ynudge
    
 
    Amount to nudge X and Y coordinates of labels by.
    
 
 
-
    max.overlaps
    
+
    max.overlaps
    
 
    passed to geom_text_repel, exclude text labels that
 overlap too many things. Defaults to 100.
    
 
 
-
    label_color
    
+
    label_color
    
 
    Color to use for text labels.
    
 
 
-
    fontface
    
+
    fontface
    
 
    font face to use for text labels (“plain”, “bold”, “italic”, “bold.italic”) (Default is "bold").
    
 
 
-
    label_size
    
+
    label_size
    
 
    text size for feature labels (passed to geom_text_repel).
    
 
 
-
    bg.color
    
+
    bg.color
    
 
    color to use for shadow/outline of text labels (passed to geom_text_repel) (Default is white).
    
 
 
-
    bg.r
    
+
    bg.r
    
 
    radius to use for shadow/outline of text labels (passed to geom_text_repel) (Default is 0.15).
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to geom_text_repel through
 LabelPoints.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # get cell bender differences data.frame
 cb_stats <- CellBender_Feature_Diff(seurat_object - obj, raw_assay = "RAW",
 cell_bender_assay = "RNA")
 
 # plot
 CellBender_Diff_Plot(feature_diff_df = cb_stats, pct_diff_threshold = 25)
-}
+} # }
 
 
    
     
    
@@ -267,15 +273,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/CellBender_Feature_Diff.html b/docs/reference/CellBender_Feature_Diff.html
index 7dd3c88ea8..8c05b47ba0 100644
--- a/docs/reference/CellBender_Feature_Diff.html
+++ b/docs/reference/CellBender_Feature_Diff.html
@@ -1,10 +1,10 @@
 
-CellBender Feature Differences — CellBender_Feature_Diff • scCustomizeCellBender Feature Differences — CellBender_Feature_Diff • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -129,40 +135,40 @@ 
    CellBender Feature Differences
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    raw_assay
    
+
    raw_assay
    
 
    Name of the assay containing the raw count data.
    
 
 
-
    cell_bender_assay
    
+
    cell_bender_assay
    
 
    Name of the assay containing the CellBender count data.
    
 
 
-
    raw_mat
    
+
    raw_mat
    
 
    Name of raw count matrix in environment if not using Seurat object.
    
 
 
-
    cell_bender_mat
    
+
    cell_bender_mat
    
 
    Name of CellBender count matrix in environment if not using Seurat object.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A data.frame containing summed raw counts, CellBender counts, count difference, and
+    
    A data.frame containing summed raw counts, CellBender counts, count difference, and
 percent difference in counts.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 cb_stats <- CellBender_Feature_Diff(seurat_object - obj, raw_assay = "RAW",
 cell_bender_assay = "RNA")
-}
+} # }
 
 
    
     
    
@@ -178,15 +184,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Cell_Highlight_Plot-1.png b/docs/reference/Cell_Highlight_Plot-1.png
index 7687bcfd71..6911555ebe 100644
Binary files a/docs/reference/Cell_Highlight_Plot-1.png and b/docs/reference/Cell_Highlight_Plot-1.png differ
diff --git a/docs/reference/Cell_Highlight_Plot.html b/docs/reference/Cell_Highlight_Plot.html
index 4165b6a765..037da5918f 100644
--- a/docs/reference/Cell_Highlight_Plot.html
+++ b/docs/reference/Cell_Highlight_Plot.html
@@ -1,9 +1,9 @@
 
-Meta Highlight Plot — Cell_Highlight_Plot • scCustomizeMeta Highlight Plot — Cell_Highlight_Plot • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Meta Highlight Plot
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -129,6 +135,7 @@ 
    Meta Highlight Plot
    
   label = FALSE,
   split.by = NULL,
   split_seurat = FALSE,
+  reduction = NULL,
   ggplot_default_colors = FALSE,
   ...
 )
    
@@ -136,73 +143,77 @@ 
    Meta Highlight Plot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    cells_highlight
    
+
    cells_highlight
    
 
    Cell names to highlight in named list.
    
 
 
-
    highlight_color
    
+
    highlight_color
    
 
    Color to highlight cells.
    
 
 
-
    background_color
    
+
    background_color
    
 
    non-highlighted cell colors (default is "lightgray")..
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    point size for both highlighted cluster and background.
    
 
 
-
    aspect_ratio
    
+
    aspect_ratio
    
 
    Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.
    
 
 
-
    figure_plot
    
+
    figure_plot
    
 
    logical.  Whether to remove the axes and plot with legend on left of plot denoting
 axes labels.  (Default is FALSE).  Requires split_seurat = TRUE.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    label
    
+
    label
    
 
    Whether to label the highlighted meta data variable(s).  Default is FALSE.
    
 
 
-
    split.by
    
+
    split.by
    
 
    Variable in @meta.data to split the plot by.
    
 
 
-
    split_seurat
    
+
    split_seurat
    
 
    logical.  Whether or not to display split plots like Seurat (shared y axis) or as
 individual plots in layout.  Default is FALSE.
    
 
 
-
    ggplot_default_colors
    
+
    reduction
    
+
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
+
+
+
    ggplot_default_colors
    
 
    logical.  If highlight_color = NULL, Whether or not to return plot
 using default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed toDimPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -210,8 +221,8 @@ 
    Examples
    
     
    library(Seurat)
 
 # Creating example non-overlapping vectors of cells
-MS4A1 <- WhichCells(object = pbmc_small, expression = MS4A1 > 4)
-GZMB <- WhichCells(object = pbmc_small, expression = GZMB > 4)
+MS4A1 <- WhichCells(object = pbmc_small, expression = MS4A1 > 4)
+GZMB <- WhichCells(object = pbmc_small, expression = GZMB > 4)
 
 # Format as named list
 cells <- list("MS4A1" = MS4A1,
@@ -234,15 +245,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Cells.html b/docs/reference/Cells.html
new file mode 100644
index 0000000000..8f4a53f195
--- /dev/null
+++ b/docs/reference/Cells.html
@@ -0,0 +1,187 @@
+
+Extract Cells from LIGER Object — Cells.liger • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Extract Cells from LIGER Object
    
+    Source: R/LIGER_Utilities.R
+    
+    
    
+
+    
    
+    
    Extract all cell barcodes from LIGER object
    
+    
    
+
+    
    
+    
    # S3 method for class 'liger'
+Cells(x, by_dataset = FALSE, ...)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    x
    
+
    LIGER object name.
    
+
+
+
    by_dataset
    
+
    logical, whether to return list with vector of cell barcodes for each
+dataset in LIGER object or to return single vector of cell barcodes across all
+datasets in object (default is FALSE; return vector of cells).
    
+
+
+
    ...
    
+
    Arguments passed to other methods
    
+
+
    
+    
    
+    
    Value
    
+    
    vector or list depending on by_dataset parameter
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+# return single vector of all cells
+all_features <- Cells(x = object, by_dataset = FALSE)
+
+# return list of vectors containing cells from each individual dataset in object
+dataset_features <- Cells(x = object, by_dataset = TRUE)
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Cells_by_Identities_LIGER.html b/docs/reference/Cells_by_Identities_LIGER.html
new file mode 100644
index 0000000000..4c05190f4d
--- /dev/null
+++ b/docs/reference/Cells_by_Identities_LIGER.html
@@ -0,0 +1,187 @@
+
+Extract Cells by identity — Cells_by_Identities_LIGER • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Extract Cells by identity
    
+    Source: R/LIGER_Utilities.R
+    
+    
    
+
+    
    
+    
    Extract all cell barcodes by identity from LIGER object
    
+    
    
+
+    
    
+    
    Cells_by_Identities_LIGER(liger_object, group.by = NULL, by_dataset = FALSE)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    liger_object
    
+
    LIGER object name.
    
+
+
+
    group.by
    
+
    name of meta data column to use, default is current default clustering.
    
+
+
+
    by_dataset
    
+
    logical, whether to return list with entries for cell barcodes for each
+identity in group.by
+or to return list of lists (1 entry per dataset and each ident within the dataset)
+(default is FALSE; return list)
    
+
+
    
+    
    
+    
    Value
    
+    
    list or list of lists depending on by_dataset parameter
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+# return single vector of all cells
+cells_by_idents <- Cells_by_Identities_LIGER(liger_object = object, by_dataset = FALSE)
+
+# return list of vectors containing cells from each individual dataset in object
+cells_by_idents_by_dataset <- Cells_by_Identities_LIGER(liger_object = object, by_dataset = TRUE)
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Cells_per_Sample.html b/docs/reference/Cells_per_Sample.html
new file mode 100644
index 0000000000..efb81978e9
--- /dev/null
+++ b/docs/reference/Cells_per_Sample.html
@@ -0,0 +1,176 @@
+
+Cells per Sample — Cells_per_Sample • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Cells per Sample
    
+    Source: R/Statistics.R
+    
+    
    
+
+    
    
+    
    Get data.frame containing the number of cells per sample.
    
+    
    
+
+    
    
+    
    Cells_per_Sample(seurat_object, sample_col = NULL)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    seurat_object
    
+
    Seurat object
    
+
+
+
    sample_col
    
+
    column name in meta.data that contains sample ID information.  Default is NULL and
+will use "orig.ident column
    
+
+
    
+    
    
+    
    Value
    
+    
    A data.frame
    
+    
    
+
+    
    
+    
    Examples
    
+    
    library(Seurat)
+num_cells <- Cells_per_Sample(seurat_object = pbmc_small, sample_col = "orig.ident")
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Change_Delim_All.html b/docs/reference/Change_Delim_All.html
index 20f2b0791f..93d4b5eac0 100644
--- a/docs/reference/Change_Delim_All.html
+++ b/docs/reference/Change_Delim_All.html
@@ -1,9 +1,9 @@
 
-Change all delimiters in cell name — Change_Delim_All • scCustomizeChange all delimiters in cell name — Change_Delim_All • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,30 +127,30 @@ 
    Change all delimiters in cell name
    
 
     
    
     
    Arguments
    
-    
    data
    
+
+
+
    data
    
 
    Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.
    
 
 
-
    current_delim
    
+
    current_delim
    
 
    a single value of current delimiter.
    
 
 
-
    new_delim
    
+
    new_delim
    
 
    a single value of new delimiter desired.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    matrix or data.frame with new column names.
    
+    
    matrix or data.frame with new column names.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 dge_matrix <- Change_Delim_All(data = dge_matrix, current_delim = ".", new_delim = "-")
-}
+} # }
 
 
    
     
    
@@ -160,15 +166,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Change_Delim_Prefix.html b/docs/reference/Change_Delim_Prefix.html
index 0aec866ccf..42a6c8f740 100644
--- a/docs/reference/Change_Delim_Prefix.html
+++ b/docs/reference/Change_Delim_Prefix.html
@@ -1,9 +1,9 @@
 
-Change barcode prefix delimiter — Change_Delim_Prefix • scCustomizeChange barcode prefix delimiter — Change_Delim_Prefix • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,30 +127,30 @@ 
    Change barcode prefix delimiter
    
 
     
    
     
    Arguments
    
-    
    data
    
+
+
+
    data
    
 
    Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.
    
 
 
-
    current_delim
    
+
    current_delim
    
 
    a single value of current delimiter.
    
 
 
-
    new_delim
    
+
    new_delim
    
 
    a single value of new delimiter desired.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    matrix or data.frame with new column names.
    
+    
    matrix or data.frame with new column names.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 dge_matrix <- Change_Delim_Prefix(data = dge_matrix, current_delim = ".", new_delim = "-")
-}
+} # }
 
 
    
     
    
@@ -160,15 +166,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Change_Delim_Suffix.html b/docs/reference/Change_Delim_Suffix.html
index fcc4e51485..ebf34028e4 100644
--- a/docs/reference/Change_Delim_Suffix.html
+++ b/docs/reference/Change_Delim_Suffix.html
@@ -1,9 +1,9 @@
 
-Change barcode suffix delimiter — Change_Delim_Suffix • scCustomizeChange barcode suffix delimiter — Change_Delim_Suffix • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,30 +127,30 @@ 
    Change barcode suffix delimiter
    
 
     
    
     
    Arguments
    
-    
    data
    
+
+
+
    data
    
 
    Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.
    
 
 
-
    current_delim
    
+
    current_delim
    
 
    a single value of current delimiter.
    
 
 
-
    new_delim
    
+
    new_delim
    
 
    a single value of new delimiter desired.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    matrix or data.frame with new column names.
    
+    
    matrix or data.frame with new column names.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 dge_matrix <- Change_Delim_Suffix(data = dge_matrix, current_delim = ".", new_delim = "-")
-}
+} # }
 
 
    
     
    
@@ -160,15 +166,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/CheckMatrix_scCustom.html b/docs/reference/CheckMatrix_scCustom.html
index 1c15334045..f56d562845 100644
--- a/docs/reference/CheckMatrix_scCustom.html
+++ b/docs/reference/CheckMatrix_scCustom.html
@@ -1,9 +1,9 @@
 
-Check Matrix Validity — CheckMatrix_scCustom • scCustomizeCheck Matrix Validity — CheckMatrix_scCustom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -124,11 +130,13 @@ 
    Check Matrix Validity
    
 
     
    
     
    Arguments
    
-    
    object
    
+
+
+
    object
    
 
    A matrix
    
 
 
-
    checks
    
+
    checks
    
 
    Type of checks to perform, choose one or more from:
    • “infinite”: Emit a warning if any value is infinite
      • 
 
    • “logical”: Emit a warning if any value is a logical
      • 
 
    • “integer”: Emit a warning if any value is not
@@ -140,11 +148,7 @@ 
      Arguments
      
 
    
     
    
     
    Value
    
-    
-
-
    Emits warnings for each test and invisibly returns NULL
    
-
-
+    
    Emits warnings for each test and invisibly returns NULL
    
     
    
     
    
     
    References
    
@@ -153,10 +157,10 @@ 
    References
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 mat <- Read10X(...)
 CheckMatrix_scCustom(object = mat)
-}
+} # }
 
 
    
     
    
@@ -172,15 +176,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Cluster_Highlight_Plot-1.png b/docs/reference/Cluster_Highlight_Plot-1.png
index 31ac688fcc..4a8c0c7549 100644
Binary files a/docs/reference/Cluster_Highlight_Plot-1.png and b/docs/reference/Cluster_Highlight_Plot-1.png differ
diff --git a/docs/reference/Cluster_Highlight_Plot.html b/docs/reference/Cluster_Highlight_Plot.html
index ce7547433c..c2a332f1ac 100644
--- a/docs/reference/Cluster_Highlight_Plot.html
+++ b/docs/reference/Cluster_Highlight_Plot.html
@@ -1,9 +1,9 @@
 
-Cluster Highlight Plot — Cluster_Highlight_Plot • scCustomizeCluster Highlight Plot — Cluster_Highlight_Plot • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
     
    
     
    Cluster Highlight Plot
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -129,6 +135,9 @@ 
    Cluster Highlight Plot
    
   label = FALSE,
   split.by = NULL,
   split_seurat = FALSE,
+  split_title_size = 15,
+  num_columns = NULL,
+  reduction = NULL,
   ggplot_default_colors = FALSE,
   ...
 )
    
@@ -136,74 +145,86 @@ 
    Cluster Highlight Plot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    cluster_name
    
+
    cluster_name
    
 
    Name(s) (or number(s)) identity of cluster to be highlighted.
    
 
 
-
    highlight_color
    
+
    highlight_color
    
 
    Color(s) to highlight cells.  The default is NULL and plot will use
 scCustomize_Palette().
    
 
 
-
    background_color
    
+
    background_color
    
 
    non-highlighted cell colors.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    point size for both highlighted cluster and background.
    
 
 
-
    aspect_ratio
    
+
    aspect_ratio
    
 
    Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.
    
 
 
-
    figure_plot
    
+
    figure_plot
    
 
    logical.  Whether to remove the axes and plot with legend on left of plot denoting
 axes labels.  (Default is FALSE).  Requires split_seurat = TRUE.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    label
    
+
    label
    
 
    Whether to label the highlighted cluster(s).  Default is FALSE.
    
 
 
-
    split.by
    
+
    split.by
    
 
    Feature to split plots by (i.e. "orig.ident").
    
 
 
-
    split_seurat
    
+
    split_seurat
    
 
    logical.  Whether or not to display split plots like Seurat (shared y axis) or as
 individual plots in layout.  Default is FALSE.
    
 
 
-
    ggplot_default_colors
    
+
    split_title_size
    
+
    size for plot title labels when using split.by.
    
+
+
+
    num_columns
    
+
    Number of columns in plot layout.  Only valid if split.by != NULL.
    
+
+
+
    reduction
    
+
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
+
+
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to DimPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -226,15 +247,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Cluster_Stats_All_Samples.html b/docs/reference/Cluster_Stats_All_Samples.html
index 3bb085af27..e4b861a1f6 100644
--- a/docs/reference/Cluster_Stats_All_Samples.html
+++ b/docs/reference/Cluster_Stats_All_Samples.html
@@ -1,9 +1,9 @@
 
-Calculate Cluster Stats — Cluster_Stats_All_Samples • scCustomizeCalculate Cluster Stats — Cluster_Stats_All_Samples • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -112,7 +118,7 @@ 
    Calculate Cluster Stats
    
     
    
 
     
    
-    
    Calculates both overall and per sample cell number and percentages per cluster based on orig.ident
    
+    
    Calculates both overall and per sample cell number and percentages per cluster based on orig.ident.
    
     
    
 
     
    
@@ -121,26 +127,26 @@ 
    Calculate Cluster Stats
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    group_by_var
    
+
    group_by_var
    
 
    meta data column to classify samples (default = "orig.ident").
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A data.frame
    
+    
    A data.frame with rows in order of frequency
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 stats <- Cluster_Stats_All_Samples(seurat_object = object, group_by_var = "orig.ident")
-}
+} # }
 
 
    
     
    
@@ -156,15 +162,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Clustered_DotPlot-1.png b/docs/reference/Clustered_DotPlot-1.png
index e850ddaa62..0ee3353ddf 100644
Binary files a/docs/reference/Clustered_DotPlot-1.png and b/docs/reference/Clustered_DotPlot-1.png differ
diff --git a/docs/reference/Clustered_DotPlot-2.png b/docs/reference/Clustered_DotPlot-2.png
index 11743bfcbb..b59fc5099d 100644
Binary files a/docs/reference/Clustered_DotPlot-2.png and b/docs/reference/Clustered_DotPlot-2.png differ
diff --git a/docs/reference/Clustered_DotPlot-3.png b/docs/reference/Clustered_DotPlot-3.png
index e850ddaa62..0ee3353ddf 100644
Binary files a/docs/reference/Clustered_DotPlot-3.png and b/docs/reference/Clustered_DotPlot-3.png differ
diff --git a/docs/reference/Clustered_DotPlot.html b/docs/reference/Clustered_DotPlot.html
index 61bc48e881..e30a53b0e4 100644
--- a/docs/reference/Clustered_DotPlot.html
+++ b/docs/reference/Clustered_DotPlot.html
@@ -1,9 +1,9 @@
 
-Clustered DotPlot — Clustered_DotPlot • scCustomizeClustered DotPlot — Clustered_DotPlot • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Clustered DotPlot
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -127,6 +133,7 @@ 
    Clustered DotPlot
    
   exp_value_type = "scaled",
   print_exp_quantiles = FALSE,
   colors_use_idents = NULL,
+  show_ident_colors = TRUE,
   x_lab_rotate = TRUE,
   plot_padding = NULL,
   flip = FALSE,
@@ -141,6 +148,13 @@ 
    Clustered DotPlot
    
   column_label_size = 8,
   legend_label_size = 10,
   legend_title_size = 10,
+  legend_position = "right",
+  legend_orientation = NULL,
+  show_ident_legend = TRUE,
+  show_row_names = TRUE,
+  show_column_names = TRUE,
+  column_names_side = "bottom",
+  row_names_side = "right",
   raster = FALSE,
   plot_km_elbow = TRUE,
   elbow_kmax = NULL,
@@ -156,60 +170,67 @@ 
    Clustered DotPlot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    features
    
+
    features
    
 
    Features to plot.
    
 
 
-
    split.by
    
+
    split.by
    
 
    Variable in @meta.data to split the identities plotted by.
    
 
 
-
    colors_use_exp
    
+
    colors_use_exp
    
 
    Color palette to use for plotting expression scale.  Default is viridis::plasma(n = 20, direction = -1).
    
 
 
-
    exp_color_min
    
+
    exp_color_min
    
 
    Minimum scaled average expression threshold (everything smaller will be set to this).
 Default is -2.
    
 
 
-
    exp_color_middle
    
+
    exp_color_middle
    
 
    What scaled expression value to use for the middle of the provided colors_use_exp.
 By default will be set to value in middle of exp_color_min and exp_color_max.
    
 
 
-
    exp_color_max
    
+
    exp_color_max
    
 
    Minimum scaled average expression threshold (everything smaller will be set to this).
 Default is 2.
    
 
 
-
    exp_value_type
    
+
    exp_value_type
    
 
    Whether to plot average normalized expression or
 scaled average normalized expression.  Only valid when split.by is provided.
    
 
 
-
    print_exp_quantiles
    
+
    print_exp_quantiles
    
 
    Whether to print the quantiles of expression data in addition to plots.
 Default is FALSE.  NOTE: These values will be altered by choices of exp_color_min and exp_color_min
 if there are values below or above those cutoffs, respectively.
    
 
 
-
    colors_use_idents
    
+
    colors_use_idents
    
 
    specify color palette to used for identity labels.  By default if
 number of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36
 will use "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.
    
 
 
-
    x_lab_rotate
    
+
    show_ident_colors
    
+
    logical, whether to show colors for idents on the column/rows of the plot
+(default is TRUE).
    
+
+
+
    x_lab_rotate
    
 
    How to rotate column labels.  By default set to TRUE which rotates labels 45 degrees.
 If set FALSE rotation is set to 0 degrees.  Users can also supply custom angle for text rotation.
    
 
 
-
    plot_padding
    
+
    plot_padding
    
 
    if plot needs extra white space padding so no plot or labels are cutoff.
 The parameter accepts TRUE or numeric vector of length 4.  If TRUE padding will be set to
 c(2, 10, 0 0) (bottom, left, top, right).  Can also be customized further with numeric
@@ -217,114 +238,140 @@ 
    Arguments
    
 Default is NULL, no padding.
    
 
 
-
    flip
    
+
    flip
    
 
    logical, whether to flip the axes of final plot.  Default is FALSE; rows = features and
 columns = idents.
    
 
 
-
    k
    
+
    k
    
 
    Value to use for k-means clustering on features  Sets (km) parameter in ComplexHeatmap::Heatmap().
 From ComplexHeatmap::Heatmap(): Apply k-means clustering on rows. If the value is larger than 1, the
 heatmap will be split by rows according to the k-means clustering. For each row slice, hierarchical
 clustering is still applied with parameters above.
    
 
 
-
    feature_km_repeats
    
+
    feature_km_repeats
    
 
    Number of k-means runs to get a consensus k-means clustering for features.
 Note if feature_km_repeats is set to value greater than one, the final number of groups might be
 smaller than row_km, but this might mean the original row_km is not a good choice.  Default is 1000.
    
 
 
-
    ident_km_repeats
    
+
    ident_km_repeats
    
 
    Number of k-means runs to get a consensus k-means clustering. Similar to
 feature_km_repeats.  Default is 1000.
    
 
 
-
    row_label_size
    
+
    row_label_size
    
 
    Size of the feature labels.  Provided to row_names_gp in Heatmap call.
    
 
 
-
    row_label_fontface
    
+
    row_label_fontface
    
 
    Fontface to use for row labels.  Provided to row_names_gp in Heatmap call.
    
 
 
-
    grid_color
    
+
    grid_color
    
 
    color to use for heatmap grid.  Default is NULL which "removes" grid by using NA color.
    
 
 
-
    cluster_feature
    
+
    cluster_feature
    
 
    logical, whether to cluster and reorder feature axis.  Default is TRUE.
    
 
 
-
    cluster_ident
    
+
    cluster_ident
    
 
    logical, whether to cluster and reorder identity axis.  Default is TRUE.
    
 
 
-
    column_label_size
    
+
    column_label_size
    
 
    Size of the feature labels.  Provided to column_names_gp in Heatmap call.
    
 
 
-
    legend_label_size
    
+
    legend_label_size
    
 
    Size of the legend text labels.  Provided to labels_gp in Heatmap legend call.
    
 
 
-
    legend_title_size
    
-
    Sise of the legend title text labels.  Provided to title_gp in Heatmap legend call.
    
+
    legend_title_size
    
+
    Size of the legend title text labels.  Provided to title_gp in Heatmap legend call.
    
+
+
+
    legend_position
    
+
    Location of the plot legend (default is "right").
    
+
 
+
    legend_orientation
    
+
    Orientation of the legend (default is NULL).
    
 
-
    raster
    
+
+
    show_ident_legend
    
+
    logical, whether to show the color legend for idents in plot (default is TRUE).
    
+
+
+
    show_row_names
    
+
    logical, whether to show row names on plot (default is TRUE).
    
+
+
+
    show_column_names
    
+
    logical, whether to show column names on plot (default is TRUE).
    
+
+
+
    column_names_side
    
+
    Should the row names be on the "bottom" or "top" of plot.  Default is "bottom".
    
+
+
+
    row_names_side
    
+
    Should the row names be on the "left" or "right" of plot.  Default is "right".
    
+
+
+
    raster
    
 
    Logical, whether to render in raster format (faster plotting, smaller files).  Default is FALSE.
    
 
 
-
    plot_km_elbow
    
+
    plot_km_elbow
    
 
    Logical, whether or not to return the Sum Squared Error Elbow Plot for k-means clustering.
 Estimating elbow of this plot is one way to determine "optimal" value for k.
 Based on: https://stackoverflow.com/a/15376462/15568251.
    
 
 
-
    elbow_kmax
    
+
    elbow_kmax
    
 
    The maximum value of k to use for plot_km_elbow.  Suggest setting larger value so the
 true shape of plot can be observed.  Value must be 1 less than number of features provided.  If NULL parameter
 will be set dependent on length of feature list up to elbow_kmax = 20.
    
 
 
-
    assay
    
+
    assay
    
 
    Name of assay to use, defaults to the active assay.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Group (color) cells in different ways (for example, orig.ident).
    
 
 
-
    idents
    
+
    idents
    
 
    Which classes to include in the plot (default is all).
    
 
 
-
    show_parent_dend_line
    
+
    show_parent_dend_line
    
 
    Logical, Sets parameter of same name in ComplexHeatmap::Heatmap().
 From ComplexHeatmap::Heatmap(): When heatmap is split, whether to add a dashed line to mark parent
 dendrogram and children dendrograms.  Default is TRUE.
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    seed
    
+
    seed
    
 
    Sets seed for reproducible plotting (ComplexHeatmap plot).
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ComplexHeatmap or if plot_km_elbow = TRUE a list containing ggplot2 object and ComplexHeatmap.
    
+    
    A ComplexHeatmap or if plot_km_elbow = TRUE a list containing ggplot2 object and ComplexHeatmap.
    
     
    
     
    
     
    References
    
@@ -370,15 +417,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/ColorBlind_Pal-1.png b/docs/reference/ColorBlind_Pal-1.png
index 4da0a87fb8..0ef99e2888 100644
Binary files a/docs/reference/ColorBlind_Pal-1.png and b/docs/reference/ColorBlind_Pal-1.png differ
diff --git a/docs/reference/ColorBlind_Pal.html b/docs/reference/ColorBlind_Pal.html
index ed8b5278d9..fc8dd50505 100644
--- a/docs/reference/ColorBlind_Pal.html
+++ b/docs/reference/ColorBlind_Pal.html
@@ -1,9 +1,9 @@
 
-Color Universal Design Short Palette — ColorBlind_Pal • scCustomizeColor Universal Design Short Palette — ColorBlind_Pal • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,9 +127,7 @@ 
    Color Universal Design Short Palette
    
 
     
    
     
    Value
    
-    
-
-
    modified/reordered color palette (8 colors) based on ditto-seq
    
+    
    modified/reordered color palette (8 colors) based on ditto-seq
    
     
    
     
    
     
    References
    
@@ -151,15 +155,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Convert_Assay.html b/docs/reference/Convert_Assay.html
index 56e0782fc1..83bd3dc3c0 100644
--- a/docs/reference/Convert_Assay.html
+++ b/docs/reference/Convert_Assay.html
@@ -1,9 +1,9 @@
 
-Convert between Seurat Assay types — Convert_Assay • scCustomizeConvert between Seurat Assay types — Convert_Assay • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,16 +127,18 @@ 
    Convert between Seurat Assay types
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    assay
    
+
    assay
    
 
    name(s) of assays to convert.  Default is NULL and will check with users
 which assays they want to convert.
    
 
 
-
    convert_to
    
+
    convert_to
    
 
    value of what assay type to convert current assays to.
 #'
    • Accepted values for V3/4 are: "Assay", "assay", "V3", or "v3".
      • 
 
    • Accepted values for V5 are: "Assay5", "assay5", "V5", or "v5".
      • 
@@ -140,13 +148,13 @@ 
      Arguments
      
 
     
      
     
      Examples
      
-    
      if (FALSE) {
+    
      if (FALSE) { # \dontrun{
 # Convert to V3/4 assay
 obj <- Convert_Assay(seurat_object = obj, convert_to = "V3")
 
 # Convert to 5 assay
 obj <- Convert_Assay(seurat_object = obj, convert_to = "V5")
-}
+} # }
 
 
      
     
      
@@ -162,15 +170,15 @@ 
      Examples
      
 
      
 
 
      
-  
      Site built with pkgdown 2.0.7.
      
+  
      Site built with pkgdown 2.1.0.
      
 
      
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Copy_From_GCP.html b/docs/reference/Copy_From_GCP.html
index 9102a147fb..7394786ff3 100644
--- a/docs/reference/Copy_From_GCP.html
+++ b/docs/reference/Copy_From_GCP.html
@@ -1,9 +1,9 @@
 
-Copy folder from GCP bucket from R Console — Copy_From_GCP • scCustomizeCopy folder from GCP bucket from R Console — Copy_From_GCP • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -121,26 +127,26 @@ 
    Copy folder from GCP bucket from R Console
    
 
     
    
     
    Arguments
    
-    
    folder_file_path
    
+
+
+
    folder_file_path
    
 
    folder to be copied to GCP bucket.
    
 
 
-
    gcp_bucket_path
    
+
    gcp_bucket_path
    
 
    GCP bucket path to copy to files.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    No return value.  Performs system copy from GCP bucket.
    
+    
    No return value.  Performs system copy from GCP bucket.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Copy_From_GCP(folder_file_path = "plots/", gcp_bucket_path = "gs://bucket_name_and_folder_path")
-}
+} # }
 
 
    
     
    
@@ -156,15 +162,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Copy_To_GCP.html b/docs/reference/Copy_To_GCP.html
index b3c73340d4..c6ceda4d5e 100644
--- a/docs/reference/Copy_To_GCP.html
+++ b/docs/reference/Copy_To_GCP.html
@@ -1,9 +1,9 @@
 
-Copy folder to GCP bucket from R Console — Copy_To_GCP • scCustomizeCopy folder to GCP bucket from R Console — Copy_To_GCP • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,26 +127,26 @@ 
    Copy folder to GCP bucket from R Console
    
 
     
    
     
    Arguments
    
-    
    folder_file_path
    
+
+
+
    folder_file_path
    
 
    folder to be copied to GCP bucket.
    
 
 
-
    gcp_bucket_path
    
+
    gcp_bucket_path
    
 
    GCP bucket path to copy to files.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    No return value.  Performs system copy to GCP bucket.
    
+    
    No return value.  Performs system copy to GCP bucket.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Copy_To_GCP(folder_file_path = "plots/", gcp_bucket_path = "gs://bucket_name_and_folder_path")
-}
+} # }
 
 
    
     
    
@@ -156,15 +162,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Create_10X_H5.html b/docs/reference/Create_10X_H5.html
index afc1f86532..5a1e4954ae 100644
--- a/docs/reference/Create_10X_H5.html
+++ b/docs/reference/Create_10X_H5.html
@@ -1,10 +1,10 @@
 
-Create H5 from 10X Outputs — Create_10X_H5 • scCustomizeCreate H5 from 10X Outputs — Create_10X_H5 • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -128,34 +134,34 @@ 
    Create H5 from 10X Outputs
    
 
     
    
     
    Arguments
    
-    
    raw_data_file_path
    
+
+
+
    raw_data_file_path
    
 
    file path to raw data file(s).
    
 
 
-
    source_type
    
+
    source_type
    
 
    type of source data (Default is "10X").  Alternatively can provide "Matrix" or "data.frame".
    
 
 
-
    save_file_path
    
+
    save_file_path
    
 
    file path to directory to save file.
    
 
 
-
    save_name
    
+
    save_name
    
 
    name prefix for output H5 file.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A HDF5 format file that will be recognized as 10X Cell Ranger formatted file by Seurat or LIGER.
    
+    
    A HDF5 format file that will be recognized as 10X Cell Ranger formatted file by Seurat or LIGER.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Create_10X_H5(raw_data_file_path = "file_path", save_file_path = "file_path2", save_name = "NAME")
-}
+} # }
 
 
    
     
    
@@ -171,15 +177,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Create_CellBender_Merged_Seurat.html b/docs/reference/Create_CellBender_Merged_Seurat.html
index 7a9ca1c1bd..7e5e77a6a8 100644
--- a/docs/reference/Create_CellBender_Merged_Seurat.html
+++ b/docs/reference/Create_CellBender_Merged_Seurat.html
@@ -1,10 +1,10 @@
 
-Create Seurat Object with Cell Bender and Raw data — Create_CellBender_Merged_Seurat • scCustomizeCreate Seurat Object with Cell Bender and Raw data — Create_CellBender_Merged_Seurat • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -130,46 +136,46 @@ 
    Create Seurat Object with Cell Bender and Raw data
    
 
     
    
     
    Arguments
    
-    
    raw_cell_bender_matrix
    
+
+
+
    raw_cell_bender_matrix
    
 
    matrix file containing the cell bender correct counts.
    
 
 
-
    raw_counts_matrix
    
+
    raw_counts_matrix
    
 
    matrix file contain the uncorrected Cell Ranger (or other) counts.
    
 
 
-
    raw_assay_name
    
+
    raw_assay_name
    
 
    a key value to use specifying the name of assay.  Default is "RAW".
    
 
 
-
    min_cells
    
-
    value to supply to min.cells parameter of CreateSeuratObject.
+
    min_cells
    
+
    value to supply to min.cells parameter of CreateSeuratObject.
 Default is 5.
    
 
 
-
    min_features
    
-
    value to supply to min.features parameter of CreateSeuratObject.
+
    min_features
    
+
    value to supply to min.features parameter of CreateSeuratObject.
 Default is 200.
    
 
 
-
    ...
    
-
    Extra parameters passed to CreateSeuratObject.
    
+
    ...
    
+
    Extra parameters passed to CreateSeuratObject.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A Seurat Object contain both the Cell Bender corrected counts ("RNA" assay) and uncorrected
+    
    A Seurat Object contain both the Cell Bender corrected counts ("RNA" assay) and uncorrected
 counts ("RAW" assay; or other name specified to raw_assay_name).
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 seurat_obj <- Create_CellBender_Merged_Seurat(raw_cell_bender_matrix = cb_matrix,
 raw_counts_matrix = cr_matrix)
-}
+} # }
 
 
    
     
    
@@ -185,15 +191,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Create_Cluster_Annotation_File.html b/docs/reference/Create_Cluster_Annotation_File.html
index 169649ffce..26fe8fc2c5 100644
--- a/docs/reference/Create_Cluster_Annotation_File.html
+++ b/docs/reference/Create_Cluster_Annotation_File.html
@@ -1,9 +1,9 @@
 
-Create cluster annotation csv file — Create_Cluster_Annotation_File • scCustomizeCreate cluster annotation csv file — Create_Cluster_Annotation_File • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -124,27 +130,27 @@ 
    Create cluster annotation csv file
    
 
     
    
     
    Arguments
    
-    
    file_path
    
+
+
+
    file_path
    
 
    path to directory to save file.  Default is current working directory.
    
 
 
-
    file_name
    
+
    file_name
    
 
    name to use for annotation file.  Function automatically adds file type ".csv" suffix.
 Default is "cluster_annotation".
    
 
 
    
     
    
     
    Value
    
-    
-
-
    No value returned.  Creates .csv file.
    
+    
    No value returned.  Creates .csv file.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Create_Cluster_Annotation_File(file_path = "cluster_annotation_folder_name")
-}
+} # }
 
 
    
     
    
@@ -160,15 +166,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Dark2_Pal-1.png b/docs/reference/Dark2_Pal-1.png
index bbe097441c..71f4dfb81a 100644
Binary files a/docs/reference/Dark2_Pal-1.png and b/docs/reference/Dark2_Pal-1.png differ
diff --git a/docs/reference/Dark2_Pal.html b/docs/reference/Dark2_Pal.html
index a63fb961bc..610df5bfca 100644
--- a/docs/reference/Dark2_Pal.html
+++ b/docs/reference/Dark2_Pal.html
@@ -1,9 +1,9 @@
 
-Dark2 Palette — Dark2_Pal • scCustomizeDark2 Palette — Dark2_Pal • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,9 +127,7 @@ 
    Dark2 Palette
    
 
     
    
     
    Value
    
-    
-
-
    "Dark2" color palette (8 colors)
    
+    
    "Dark2" color palette (8 colors)
    
     
    
     
    
     
    References
    
@@ -152,15 +156,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/DimPlot_All_Samples-1.png b/docs/reference/DimPlot_All_Samples-1.png
index 26e914dc37..d3f2ee3df7 100644
Binary files a/docs/reference/DimPlot_All_Samples-1.png and b/docs/reference/DimPlot_All_Samples-1.png differ
diff --git a/docs/reference/DimPlot_All_Samples.html b/docs/reference/DimPlot_All_Samples.html
index f6d92ae32f..9f84b1996b 100644
--- a/docs/reference/DimPlot_All_Samples.html
+++ b/docs/reference/DimPlot_All_Samples.html
@@ -1,9 +1,9 @@
 
-DimPlot by Meta Data Column — DimPlot_All_Samples • scCustomizeDimPlot by Meta Data Column — DimPlot_All_Samples • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    DimPlot by Meta Data Column
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -134,62 +140,62 @@ 
    DimPlot by Meta Data Column
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    meta_data_column
    
+
    meta_data_column
    
 
    Meta data column to split plots by.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    single color to use for all plots or a vector of colors equal to the number of plots.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    aspect_ratio
    
+
    aspect_ratio
    
 
    Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.
    
 
 
-
    title_size
    
+
    title_size
    
 
    size for plot title labels.
    
 
 
-
    num_columns
    
+
    num_columns
    
 
    number of columns in final layout plot.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
 
 
-
    dims
    
+
    dims
    
 
    Which dimensions to plot.  Defaults to c(1,2) if not specified.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to DimPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -216,15 +222,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/DimPlot_LIGER.html b/docs/reference/DimPlot_LIGER.html
index 77ac12eac3..a9fd6feafc 100644
--- a/docs/reference/DimPlot_LIGER.html
+++ b/docs/reference/DimPlot_LIGER.html
@@ -1,9 +1,9 @@
 
-DimPlot LIGER Version — DimPlot_LIGER • scCustomizeDimPlot LIGER Version — DimPlot_LIGER • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -126,6 +132,7 @@ 
    DimPlot LIGER Version
    
   shuffle = TRUE,
   shuffle_seed = 1,
   reduction_label = "UMAP",
+  reduction = NULL,
   aspect_ratio = NULL,
   label = TRUE,
   label_size = NA,
@@ -143,116 +150,122 @@ 
    DimPlot LIGER Version
    
 
     
    
     
    Arguments
    
-    
    liger_object
    
+
+
+
    liger_object
    
 
    liger liger_object.  Need to perform clustering before calling this function
    
 
 
-
    group_by
    
+
    group_by
    
 
    Variable to be plotted.  If NULL will plot clusters from liger@clusters slot.
 If combination = TRUE will plot both clusters and meta data variable.
    
 
 
-
    split_by
    
+
    split_by
    
 
    Variable to split plots by.
    
 
 
-
    colors_use_cluster
    
+
    colors_use_cluster
    
 
    colors to use for plotting by clusters.  By default if number of levels plotted is
 less than or equal to 36 will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE
 both from DiscretePalette_scCustomize.
    
 
 
-
    colors_use_meta
    
+
    colors_use_meta
    
 
    colors to use for plotting by meta data (cell.data) variable.  By default if number
 of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36 will use
 "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.
    
 
 
-
    pt_size
    
+
    pt_size
    
 
    Adjust point size for plotting.
    
 
 
-
    shuffle
    
+
    shuffle
    
 
    logical. Whether to randomly shuffle the order of points. This can be useful for crowded plots
 if points of interest are being buried. (Default is TRUE).
    
 
 
-
    shuffle_seed
    
+
    shuffle_seed
    
 
    Sets the seed if randomly shuffling the order of points.
    
 
 
-
    reduction_label
    
+
    reduction_label
    
 
    What to label the x and y axes of resulting plots.  LIGER does not store name of
-technique and therefore needs to be set manually.  Default is "UMAP".
    
+technique and therefore needs to be set manually.  Default is "UMAP". (only valid for
+rliger < 2.0.0).
    
+
+
+
    reduction
    
+
    specify reduction to use when plotting.  Default is current object
+default reduction (only valid for rliger v2.0.0 or greater).
    
 
 
-
    aspect_ratio
    
+
    aspect_ratio
    
 
    Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.
    
 
 
-
    label
    
+
    label
    
 
    logical.  Whether or not to label the clusters.  ONLY applies to plotting by cluster.  Default is TRUE.
    
 
 
-
    label_size
    
+
    label_size
    
 
    size of cluster labels.
    
 
 
-
    label_repel
    
+
    label_repel
    
 
    logical.  Whether to repel cluster labels from each other if plotting by
 cluster (if group_by = NULL or group_by = "cluster).  Default is FALSE.
    
 
 
-
    label_box
    
+
    label_box
    
 
    logical.  Whether to put a box around the label text (uses geom_text vs geom_label).
 Default is FALSE.
    
 
 
-
    label_color
    
+
    label_color
    
 
    Color to use for cluster labels.  Default is "black".
    
 
 
-
    combination
    
+
    combination
    
 
    logical, whether to return patchwork displaying both plots side by side.  (Default is FALSE).
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    num_columns
    
+
    num_columns
    
 
    Number of columns in plot layout.  Only valid if split.by != NULL.
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot/patchwork object
    
+    
    A ggplot/patchwork object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 DimPlot_LIGER(liger_object = obj_name, reduction_label = "UMAP")
-}
+} # }
 
 
    
     
    
@@ -268,15 +281,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/DimPlot_scCustom-1.png b/docs/reference/DimPlot_scCustom-1.png
index 68ac4ca57e..955978515e 100644
Binary files a/docs/reference/DimPlot_scCustom-1.png and b/docs/reference/DimPlot_scCustom-1.png differ
diff --git a/docs/reference/DimPlot_scCustom.html b/docs/reference/DimPlot_scCustom.html
index f8ce058692..4576630697 100644
--- a/docs/reference/DimPlot_scCustom.html
+++ b/docs/reference/DimPlot_scCustom.html
@@ -1,9 +1,9 @@
 
-DimPlot with modified default settings — DimPlot_scCustom • scCustomizeDimPlot with modified default settings — DimPlot_scCustom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    DimPlot with modified default settings
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -126,6 +132,10 @@ 
    DimPlot with modified default settings
    
   split_seurat = FALSE,
   figure_plot = FALSE,
   aspect_ratio = NULL,
+  add_prop_plot = FALSE,
+  prop_plot_percent = FALSE,
+  prop_plot_x_log = FALSE,
+  prop_plot_label = FALSE,
   shuffle = TRUE,
   seed = 1,
   label = NULL,
@@ -145,115 +155,134 @@ 
    DimPlot with modified default settings
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    color palette to use for plotting.  By default if number of levels plotted is less than
 or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE
 both from DiscretePalette_scCustomize.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.
    
 
 
-
    split.by
    
+
    split.by
    
 
    Feature to split plots by (i.e. "orig.ident").
    
 
 
-
    split_seurat
    
+
    split_seurat
    
 
    logical.  Whether or not to display split plots like Seurat (shared y axis) or as
 individual plots in layout.  Default is FALSE.
    
 
 
-
    figure_plot
    
+
    figure_plot
    
 
    logical.  Whether to remove the axes and plot with legend on left of plot denoting
 axes labels.  (Default is FALSE).  Requires split_seurat = TRUE.
    
 
 
-
    aspect_ratio
    
+
    aspect_ratio
    
 
    Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.
    
 
 
-
    shuffle
    
+
    add_prop_plot
    
+
    logical, whether to add plot to returned layout with the number of cells per identity
+(or percent of cells per identity).  Default is FALSE.
    
+
+
+
    prop_plot_percent
    
+
    logical, if add_prop_plot = TRUE this parameter controls whether
+proportion plot shows raw cell number or percent of cells per identity.  Default is FALSE; plots raw cell number.
    
+
+
+
    prop_plot_x_log
    
+
    logical, if add_prop_plot = TRUE this parameter controls whether to change x axis
+to log10 scale (Default is FALSE).
    
+
+
+
    prop_plot_label
    
+
    logical, if add_prop_plot = TRUE this parameter controls whether to label the bars with total number of cells or percentages; Default is FALSE.
    
+
+
+
    shuffle
    
 
    logical. Whether to randomly shuffle the order of points. This can be useful for crowded
 plots if points of interest are being buried. (Default is TRUE).
    
 
 
-
    seed
    
+
    seed
    
 
    Sets the seed if randomly shuffling the order of points.
    
 
 
-
    label
    
+
    label
    
 
    Whether to label the clusters.  By default if group.by = NULL label = TRUE, and
 otherwise it is FALSE.
    
 
 
-
    label.size
    
+
    label.size
    
 
    Sets size of labels.
    
 
 
-
    label.color
    
+
    label.color
    
 
    Sets the color of the label text.
    
 
 
-
    label.box
    
+
    label.box
    
 
    Whether to put a box around the label text (geom_text vs geom_label).
    
 
 
-
    dims
    
+
    dims
    
 
    Which dimensions to plot.  Defaults to c(1,2) if not specified.
    
 
 
-
    repel
    
+
    repel
    
 
    Repel labels.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    num_columns
    
+
    num_columns
    
 
    Number of columns in plot layout.  Only valid if split.by != NULL.
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to DimPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
     
    
     
    References
    
@@ -282,15 +311,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/DiscretePalette_scCustomize-1.png b/docs/reference/DiscretePalette_scCustomize-1.png
index 1c1f7ad7f0..d9ed012b42 100644
Binary files a/docs/reference/DiscretePalette_scCustomize-1.png and b/docs/reference/DiscretePalette_scCustomize-1.png differ
diff --git a/docs/reference/DiscretePalette_scCustomize.html b/docs/reference/DiscretePalette_scCustomize.html
index 9ec2eff719..92109e1944 100644
--- a/docs/reference/DiscretePalette_scCustomize.html
+++ b/docs/reference/DiscretePalette_scCustomize.html
@@ -1,9 +1,9 @@
 
-Discrete color palettes — DiscretePalette_scCustomize • scCustomizeDiscrete color palettes — DiscretePalette_scCustomize • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -126,29 +132,29 @@ 
    Discrete color palettes
    
 
     
    
     
    Arguments
    
-    
    num_colors
    
+
+
+
    num_colors
    
 
    Number of colors to be generated.
    
 
 
-
    palette
    
+
    palette
    
 
    Options are
 "alphabet", "alphabet2", "glasbey", "polychrome", "stepped", "ditto_seq", "varibow".
    
 
 
-
    shuffle_pal
    
+
    shuffle_pal
    
 
    randomly shuffle the outputted palette.  Most useful for varibow palette as
 that is normally an ordered palette.
    
 
 
-
    seed
    
+
    seed
    
 
    random seed for the palette shuffle.  Default = 123.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A vector of colors
    
+    
    A vector of colors
    
     
    
     
    
     
    References
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/DotPlot_scCustom-1.png b/docs/reference/DotPlot_scCustom-1.png
index f2b6153e2c..3756decacb 100644
Binary files a/docs/reference/DotPlot_scCustom-1.png and b/docs/reference/DotPlot_scCustom-1.png differ
diff --git a/docs/reference/DotPlot_scCustom.html b/docs/reference/DotPlot_scCustom.html
index 2736efbd90..9d0a6c1776 100644
--- a/docs/reference/DotPlot_scCustom.html
+++ b/docs/reference/DotPlot_scCustom.html
@@ -1,9 +1,9 @@
 
-Customized DotPlot — DotPlot_scCustom • scCustomizeCustomized DotPlot — DotPlot_scCustom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Customized DotPlot
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -132,52 +138,52 @@ 
    Customized DotPlot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    features
    
+
    features
    
 
    Features to plot.
    
 
 
-
    group.by
    
-
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
+
    group.by
    
+
    Name of metadata variable (column) to group cells by (for example, orig.ident);
 default is the current active.ident of the object.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    specify color palette to used.  Default is viridis_plasma_dark_high.
    
 
 
-
    remove_axis_titles
    
+
    remove_axis_titles
    
 
    logical. Whether to remove the x and y axis titles.  Default = TRUE.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    Rotate x-axis labels 45 degrees (Default is FALSE).
    
 
 
-
    y_lab_rotate
    
+
    y_lab_rotate
    
 
    Rotate x-axis labels 45 degrees (Default is FALSE).
    
 
 
-
    facet_label_rotate
    
+
    facet_label_rotate
    
 
    Rotate facet labels on grouped DotPlots by 45 degrees (Default is FALSE).
    
 
 
-
    flip_axes
    
+
    flip_axes
    
 
    whether or not to flip and X and Y axes (Default is FALSE).
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to DotPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -205,15 +211,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Embeddings.html b/docs/reference/Embeddings.html
new file mode 100644
index 0000000000..dc7e4a090d
--- /dev/null
+++ b/docs/reference/Embeddings.html
@@ -0,0 +1,193 @@
+
+Extract matrix of embeddings — Embeddings.liger • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Extract matrix of embeddings
    
+    Source: R/LIGER_Utilities.R
+    
+    
    
+
+    
    
+    
    Extract matrix containing iNMF or dimensionality reduction embeddings.
    
+    
    
+
+    
    
+    
    # S3 method for class 'liger'
+Embeddings(object, reduction = NULL, iNMF = FALSE, check_only = FALSE, ...)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    object
    
+
    LIGER object name.
    
+
+
+
    reduction
    
+
    name of dimensionality reduction to pull
    
+
+
+
    iNMF
    
+
    logical, whether to extract iNMF h.norm matrix instead of dimensionality reduction embeddings.
    
+
+
+
    check_only
    
+
    logical, return TRUE if valid reduction is present.
    
+
+
+
    ...
    
+
    Arguments passed to other methods
    
+
+
    
+    
    
+    
    Value
    
+    
    matrix
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+# Extract embedding matrix for current dimensionality reduction
+UMAP_coord <- Embeddings(object = liger_object)
+
+# Extract iNMF h.norm matrix
+iNMF_mat <- Embeddings(object = liger_object, reduction = "iNMF")
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Extract_Modality.html b/docs/reference/Extract_Modality.html
index 0154f5790e..336276bd73 100644
--- a/docs/reference/Extract_Modality.html
+++ b/docs/reference/Extract_Modality.html
@@ -1,10 +1,10 @@
 
-Extract multi-modal data into list by modality — Extract_Modality • scCustomizeExtract multi-modal data into list by modality — Extract_Modality • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -123,23 +129,23 @@ 
    Extract multi-modal data into list by modality
    
 
     
    
     
    Arguments
    
-    
    matrix_list
    
+
+
+
    matrix_list
    
 
    list of matrices to split by modality
    
 
 
    
     
    
     
    Value
    
-    
-
-
    list of lists, with one sublist per data modality.  Sub-list contain 1 matrix entry per sample
    
+    
    list of lists, with one sublist per data modality.  Sub-list contain 1 matrix entry per sample
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 multi_mat <- Read10X(...)
 new_multi_mat <- Extract_Modality(matrix_list = multi_mat)
-}
+} # }
 
 
    
     
    
@@ -155,15 +161,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Extract_Sample_Meta.html b/docs/reference/Extract_Sample_Meta.html
index eb13b3e5d1..e0819deb20 100644
--- a/docs/reference/Extract_Sample_Meta.html
+++ b/docs/reference/Extract_Sample_Meta.html
@@ -1,10 +1,10 @@
 
-Extract sample level meta.data — Extract_Sample_Meta • scCustomizeExtract sample level meta.data — Extract_Sample_Meta • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -129,21 +135,23 @@ 
    Extract sample level meta.data
    
 
     
    
     
    Arguments
    
-    
    object
    
+
+
+
    object
    
 
    Seurat object
    
 
 
-
    sample_name
    
+
    sample_name
    
 
    meta.data column to use as sample.  Output data.frame will contain one row per
 level or unique value in this variable.
    
 
 
-
    variables_include
    
+
    variables_include
    
 
    @meta.data columns to keep in final data.frame.  All other columns will
 be discarded.  Default is NULL.
    
 
 
-
    variables_exclude
    
+
    variables_exclude
    
 
    columns to discard in final data.frame.  Many cell level columns are
 irrelevant at the sample level (e.g., nFeature_RNA, percent_mito).
    • Default parameter value is NULL but internally will set to discard nFeature_ASSAY(s),
 nCount_ASSAY(s), percent_mito, percent_ribo, percent_mito_ribo, and log10GenesPerUMI.
      • 
@@ -153,16 +161,14 @@ 
      Arguments
      
 
    
 
 
-
    include_all
    
+
    include_all
    
 
    logical, whether or not to include all object meta data columns in output data.frame.
 Default is FALSE.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Returns a data.frame with one row per sample_name.
    
+    
    Returns a data.frame with one row per sample_name.
    
     
    
 
     
    
@@ -194,15 +200,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Extract_Top_Markers.html b/docs/reference/Extract_Top_Markers.html
index b75aa0d9e0..9c90bf7a46 100644
--- a/docs/reference/Extract_Top_Markers.html
+++ b/docs/reference/Extract_Top_Markers.html
@@ -1,10 +1,10 @@
 
-Extract Top N Marker Genes — Extract_Top_Markers • scCustomizeExtract Top N Marker Genes — Extract_Top_Markers • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -133,62 +139,62 @@ 
    Extract Top N Marker Genes
    
 
     
    
     
    Arguments
    
-    
    marker_dataframe
    
+
+
+
    marker_dataframe
    
 
    data.frame output from FindAllMarkers or similar analysis.
    
 
 
-
    num_genes
    
+
    num_genes
    
 
    number of genes per group (e.g., cluster) to include in output list.
    
 
 
-
    group_by
    
+
    group_by
    
 
    column name of marker_dataframe to group data by.  Default is "cluster" based on
 FindAllMarkers.
    
 
 
-
    rank_by
    
+
    rank_by
    
 
    column name of marker_dataframe to rank data by when selecting num_genes per group_by.
 Default is "avg_log2FC" based on FindAllMarkers.
    
 
 
-
    gene_column
    
+
    gene_column
    
 
    column name of marker_dataframe that contains the gene IDs.  Default is "gene"
 based on FindAllMarkers.
    
 
 
-
    gene_rownames_to_column
    
+
    gene_rownames_to_column
    
 
    logical. Whether gene IDs are stored in rownames and should be moved to
 column.  Default is FALSE.
    
 
 
-
    data_frame
    
+
    data_frame
    
 
    Logical, whether or not to return filtered data.frame of the original markers_dataframe or
 to return a vector of gene IDs.  Default is FALSE.
    
 
 
-
    named_vector
    
+
    named_vector
    
 
    Logical, whether or not to name the vector of gene names that is returned by the function.
 If TRUE will name the vector using the column provided to group_by.  Default is TRUE.
    
 
 
-
    make_unique
    
+
    make_unique
    
 
    Logical, whether an unnamed vector should return only unique values.  Default is FALSE.
 Not applicable when data_frame = TRUE or named_vector = TRUE.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    filtered data.frame, vector, or named vector containing gene IDs.
    
+    
    filtered data.frame, vector, or named vector containing gene IDs.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 top10_genes <- Extract_Top_Markers(marker_dataframe = markers_results, num_genes = 10,
 group_by = "cluster", rank_by = "avg_log2FC")
-}
+} # }
 
 
    
     
    
@@ -204,15 +210,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Factor_Cor_Plot.html b/docs/reference/Factor_Cor_Plot.html
new file mode 100644
index 0000000000..045513a160
--- /dev/null
+++ b/docs/reference/Factor_Cor_Plot.html
@@ -0,0 +1,246 @@
+
+Factor Correlation Plot — Factor_Cor_Plot • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Factor Correlation Plot
    
+    Source: R/LIGER_Plotting.R
+    
+    
    
+
+    
    
+    
    Plot positive correlations between gene loadings across W factor matrix in liger or
+feature loadings in reduction slot of Seurat object.
+Any negative correlations are set to NA and NA values set to bottom color of color gradient.
    
+    
    
+
+    
    
+    
    Factor_Cor_Plot(
+  object,
+  colors_use = NULL,
+  label = FALSE,
+  label_threshold = 0.5,
+  label_size = 5,
+  plot_title = NULL,
+  plot_type = "full",
+  positive_only = FALSE,
+  x_lab_rotate = TRUE,
+  cluster = TRUE,
+  cluster_rect = FALSE,
+  cluster_rect_num = NULL,
+  cluster_rect_col = NULL
+)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    object
    
+
    liger or Seurat object.
    
+
+
+
    colors_use
    
+
    Color palette to use for correlation values.
+Default is RColorBrewer::RdBu if positive_only = FALSE.
+If positive_only = TRUE the default is viridis.
+Users can also supply vector of 3 colors (low, mid, high).
    
+
+
+
    label
    
+
    logical, whether to add correlation values to plot result.
    
+
+
+
    label_threshold
    
+
    threshold for adding correlation values if label = TRUE.  Default
+is 0.5.
    
+
+
+
    label_size
    
+
    size of correlation labels
    
+
+
+
    plot_title
    
+
    Plot title.
    
+
+
+
    plot_type
    
+
    Controls plotting full matrix, or just the upper or lower triangles.
+Accepted values are: "full" (default), "upper", or "lower".
    
+
+
+
    positive_only
    
+
    logical, whether to limit the plotted values to only positive
+correlations (negative values set to 0); default is FALSE.
    
+
+
+
    x_lab_rotate
    
+
    logical, whether to rotate the axes labels on the x-axis.  Default is TRUE.
    
+
+
+
    cluster
    
+
    logical, whether to cluster the plot using hclust (default TRUE).  If FALSE
+factors are listed in numerical order.
    
+
+
+
    cluster_rect
    
+
    logical, whether to add rectangles around the clustered areas on plot,
+default is FALSE.
    
+
+
+
    cluster_rect_num
    
+
    number of rectangles to add to the plot, default NULL.
    
+
+
+
    cluster_rect_col
    
+
    color to use for rectangles, default MULL (will set color automatically).
    
+
+
    
+    
    
+    
    Value
    
+    
    A ggplot object
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+Factor_Cor_Plot(object = obj)
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/FeaturePlot_DualAssay.html b/docs/reference/FeaturePlot_DualAssay.html
index 4a00361ca8..3826b63f89 100644
--- a/docs/reference/FeaturePlot_DualAssay.html
+++ b/docs/reference/FeaturePlot_DualAssay.html
@@ -1,10 +1,10 @@
 
-Customize FeaturePlot of two assays — FeaturePlot_DualAssay • scCustomizeCustomize FeaturePlot of two assays — FeaturePlot_DualAssay • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Customize FeaturePlot of two assays
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -124,6 +130,7 @@ 
    Customize FeaturePlot of two assays
    
   assay1 = "RAW",
   assay2 = "RNA",
   colors_use = viridis_plasma_dark_high,
+  colors_use_assay2 = NULL,
   na_color = "lightgray",
   order = TRUE,
   pt.size = NULL,
@@ -132,7 +139,6 @@ 
    Customize FeaturePlot of two assays
    
   na_cutoff = 1e-09,
   raster = NULL,
   raster.dpi = c(512, 512),
-  slot = deprecated(),
   layer = "data",
   num_columns = NULL,
   alpha_exp = NULL,
@@ -143,102 +149,102 @@ 
    Customize FeaturePlot of two assays
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    features
    
+
    features
    
 
    Feature(s) to plot.
    
 
 
-
    assay1
    
+
    assay1
    
 
    name of assay one.  Default is "RAW" as featured in Create_CellBender_Merged_Seurat
    
 
 
-
    assay2
    
+
    assay2
    
 
    name of assay two  Default is "RNA" as featured in Create_CellBender_Merged_Seurat
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    list of colors or color palette to use.
    
 
 
-
    na_color
    
+
    colors_use_assay2
    
+
    optional, a second color palette to use for the second assay.
    
+
+
+
    na_color
    
 
    color to use for points below lower limit.
    
 
 
-
    order
    
+
    order
    
 
    whether to move positive cells to the top (default = TRUE).
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    aspect_ratio
    
+
    aspect_ratio
    
 
    Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
 
 
-
    na_cutoff
    
+
    na_cutoff
    
 
    Value to use as minimum expression cutoff.  To set no cutoff set to NA.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    slot
    
-
    [Deprecated] soft-deprecated.  See layer
    
-
-
-
    layer
    
+
    layer
    
 
    Which layer to pull expression data from?  Default is "data".
    
 
 
-
    num_columns
    
+
    num_columns
    
 
    Number of columns in plot layout.  If number of features > 1 then num_columns
 dictates the number of columns in overall layout (num_columns = 1 means stacked layout & num_columns = 2
 means adjacent layout).
    
 
 
-
    alpha_exp
    
+
    alpha_exp
    
 
    new alpha level to apply to expressing cell color palette (colors_use).  Must be
 value between 0-1.
    
 
 
-
    alpha_na_exp
    
+
    alpha_na_exp
    
 
    new alpha level to apply to non-expressing cell color palette (na_color).  Must be
 value between 0-1.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to FeaturePlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 FeaturePlot_DualAssay(seurat_object = object, features = "Cx3cr1", assay1 = "RAW", assay2 = "RNA",
 colors_use = viridis_plasma_dark_high, na_color = "lightgray")
-}
+} # }
 
 
    
     
    
@@ -254,15 +260,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/FeaturePlot_scCustom-1.png b/docs/reference/FeaturePlot_scCustom-1.png
index 7f00e645f4..c940dac986 100644
Binary files a/docs/reference/FeaturePlot_scCustom-1.png and b/docs/reference/FeaturePlot_scCustom-1.png differ
diff --git a/docs/reference/FeaturePlot_scCustom.html b/docs/reference/FeaturePlot_scCustom.html
index 3f7be41ef1..6f51092391 100644
--- a/docs/reference/FeaturePlot_scCustom.html
+++ b/docs/reference/FeaturePlot_scCustom.html
@@ -1,9 +1,9 @@
 
-Customize FeaturePlot — FeaturePlot_scCustom • scCustomizeCustomize FeaturePlot — FeaturePlot_scCustom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Customize FeaturePlot
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -132,7 +138,6 @@ 
    Customize FeaturePlot
    
   aspect_ratio = NULL,
   figure_plot = FALSE,
   num_columns = NULL,
-  slot = deprecated(),
   layer = "data",
   alpha_exp = NULL,
   alpha_na_exp = NULL,
@@ -145,115 +150,111 @@ 
    Customize FeaturePlot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    features
    
+
    features
    
 
    Feature(s) to plot.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    list of colors or color palette to use.
    
 
 
-
    na_color
    
+
    na_color
    
 
    color to use for points below lower limit.
    
 
 
-
    order
    
+
    order
    
 
    whether to move positive cells to the top (default = TRUE).
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
 
 
-
    na_cutoff
    
+
    na_cutoff
    
 
    Value to use as minimum expression cutoff.  This will be lowest value plotted use
 palette provided to colors_use.  Leave as default value to plot only positive non-zero values using
 color scale and zero/negative values as NA.  To plot all values using color palette set to NA.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    split.by
    
+
    split.by
    
 
    Variable in @meta.data to split the plot by.
    
 
 
-
    split_collect
    
+
    split_collect
    
 
    logical, whether to collect the legends/guides when plotting with split.by.
 Default is TRUE if one value is provided to features otherwise is set to FALSE.
    
 
 
-
    aspect_ratio
    
+
    aspect_ratio
    
 
    Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.
    
 
 
-
    figure_plot
    
+
    figure_plot
    
 
    logical.  Whether to remove the axes and plot with legend on left of plot denoting
 axes labels.  (Default is FALSE).  Requires split_seurat = TRUE.
    
 
 
-
    num_columns
    
+
    num_columns
    
 
    Number of columns in plot layout.
    
 
 
-
    slot
    
-
    [Deprecated] soft-deprecated.  See layer
    
-
-
-
    layer
    
+
    layer
    
 
    Which layer to pull expression data from?  Default is "data".
    
 
 
-
    alpha_exp
    
+
    alpha_exp
    
 
    new alpha level to apply to expressing cell color palette (colors_use).  Must be
 value between 0-1.
    
 
 
-
    alpha_na_exp
    
+
    alpha_na_exp
    
 
    new alpha level to apply to non-expressing cell color palette (na_color).  Must be
 value between 0-1.
    
 
 
-
    label
    
+
    label
    
 
    logical, whether to label the clusters.  Default is FALSE.
    
 
 
-
    label_feature_yaxis
    
+
    label_feature_yaxis
    
 
    logical, whether to place feature labels on secondary y-axis as opposed to
 above legend key.  Default is FALSE.  When setting label_feature_yaxis = TRUE the number of columns
 in plot output will automatically be set to the number of levels in split.by'
    
 
 
-
    combine
    
+
    combine
    
 
    Combine plots into a single patchworked ggplot object.
 If FALSE, return a list of ggplot objects.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to FeaturePlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -286,15 +287,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/FeatureScatter_scCustom-1.png b/docs/reference/FeatureScatter_scCustom-1.png
index e7678e4c08..6aed93c444 100644
Binary files a/docs/reference/FeatureScatter_scCustom-1.png and b/docs/reference/FeatureScatter_scCustom-1.png differ
diff --git a/docs/reference/FeatureScatter_scCustom.html b/docs/reference/FeatureScatter_scCustom.html
index 633d4ba013..943f11684b 100644
--- a/docs/reference/FeatureScatter_scCustom.html
+++ b/docs/reference/FeatureScatter_scCustom.html
@@ -1,9 +1,9 @@
 
-Modified version of FeatureScatter — FeatureScatter_scCustom • scCustomizeModified version of FeatureScatter — FeatureScatter_scCustom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Modified version of FeatureScatter
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -120,6 +126,7 @@ 
    Modified version of FeatureScatter
    
   seurat_object,
   feature1 = NULL,
   feature2 = NULL,
+  cells = NULL,
   colors_use = NULL,
   pt.size = NULL,
   group.by = NULL,
@@ -140,90 +147,94 @@ 
    Modified version of FeatureScatter
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    feature1
    
+
    feature1
    
 
    First feature to plot.
    
 
 
-
    feature2
    
+
    feature2
    
 
    Second feature to plot.
    
 
 
-
    colors_use
    
+
    cells
    
+
    Cells to include on the scatter plot.
    
+
+
+
    colors_use
    
 
    color for the points on plot.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident).
 Default is active ident.
    
 
 
-
    split.by
    
+
    split.by
    
 
    Feature to split plots by (i.e. "orig.ident").
    
 
 
-
    split_seurat
    
+
    split_seurat
    
 
    logical.  Whether or not to display split plots like Seurat (shared y axis) or as
 individual plots in layout.  Default is FALSE.
    
 
 
-
    shuffle
    
+
    shuffle
    
 
    logical, whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. Default is TRUE.
    
 
 
-
    aspect_ratio
    
+
    aspect_ratio
    
 
    Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.
    
 
 
-
    title_size
    
+
    title_size
    
 
    size for plot title labels. Does NOT apply if split_seurat = TRUE.
    
 
 
-
    plot.cor
    
+
    plot.cor
    
 
    Display correlation in plot subtitle (or title if split_seurat = TRUE).
    
 
 
-
    num_columns
    
+
    num_columns
    
 
    number of columns in final layout plot.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to FeatureScatter.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -258,15 +269,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Feature_Present.html b/docs/reference/Feature_Present.html
index 12e69ae740..a6bde2a3ed 100644
--- a/docs/reference/Feature_Present.html
+++ b/docs/reference/Feature_Present.html
@@ -1,10 +1,10 @@
 
-Check if genes/features are present — Feature_Present • scCustomizeCheck if genes/features are present — Feature_Present • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -132,59 +138,59 @@ 
    Check if genes/features are present
    
 
     
    
     
    Arguments
    
-    
    data
    
+
+
+
    data
    
 
    Name of input data.  Currently only data of classes: Seurat, liger, data.frame,
 dgCMatrix, dgTMatrix, tibble are accepted.  Gene_IDs must be present in rownames of the data.
    
 
 
-
    features
    
+
    features
    
 
    vector of features to check.
    
 
 
-
    case_check
    
+
    case_check
    
 
    logical. Whether or not to check if features are found if the case is changed from the
 input list (Sentence case to Upper and vice versa).  Default is TRUE.
    
 
 
-
    case_check_msg
    
+
    case_check_msg
    
 
    logical. Whether to print message to console if alternate case features are found
 in addition to inclusion in returned list.  Default is TRUE.
    
 
 
-
    print_msg
    
+
    print_msg
    
 
    logical. Whether message should be printed if all features are found.  Default is TRUE.
    
 
 
-
    omit_warn
    
+
    omit_warn
    
 
    logical. Whether to print message about features that are not found in current object.
 Default is TRUE.
    
 
 
-
    return_none
    
+
    return_none
    
 
    logical. Whether list of found vs. bad features should still be returned if no
 features are found.  Default is FALSE.
    
 
 
-
    seurat_assay
    
+
    seurat_assay
    
 
    Name of assay to pull feature names from if data is Seurat Object.
 Default is NULL which will check against features from all assays present.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A list of length 3 containing 1) found features, 2) not found features, 3) features found if
+    
    A list of length 3 containing 1) found features, 2) not found features, 3) features found if
 case was modified.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 features <- Feature_Present(data = obj_name, features = DEG_list, print_msg = TRUE,
 case_check = TRUE)
 found_features <- features[[1]]
-}
+} # }
 
 
    
     
    
@@ -200,15 +206,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Features.html b/docs/reference/Features.html
new file mode 100644
index 0000000000..1fdb9d830a
--- /dev/null
+++ b/docs/reference/Features.html
@@ -0,0 +1,187 @@
+
+Extract Features from LIGER Object — Features.liger • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Extract Features from LIGER Object
    
+    Source: R/LIGER_Utilities.R
+    
+    
    
+
+    
    
+    
    Extract all unique features from LIGER object
    
+    
    
+
+    
    
+    
    # S3 method for class 'liger'
+Features(x, by_dataset = FALSE, ...)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    x
    
+
    LIGER object name.
    
+
+
+
    by_dataset
    
+
    logical, whether to return list with vector of features for each dataset in
+LIGER object or to return single vector of unique features across all datasets in object
+(default is FALSE; return vector of unique features)
    
+
+
+
    ...
    
+
    Arguments passed to other methods
    
+
+
    
+    
    
+    
    Value
    
+    
    vector or list depending on by_dataset parameter
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+# return single vector of all unique features
+all_features <- Features(x = object, by_dataset = FALSE)
+
+# return list of vectors containing features from each individual dataset in object
+dataset_features <- Features(x = object, by_dataset = TRUE)
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Fetch_Meta.Seurat.html b/docs/reference/Fetch_Meta.Seurat.html
new file mode 100644
index 0000000000..918037aa65
--- /dev/null
+++ b/docs/reference/Fetch_Meta.Seurat.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Fetch_Meta.html b/docs/reference/Fetch_Meta.html
index 12f376640a..8249f36349 100644
--- a/docs/reference/Fetch_Meta.html
+++ b/docs/reference/Fetch_Meta.html
@@ -1,9 +1,9 @@
 
-Get meta data from object — Fetch_Meta • scCustomizeGet meta data from object — Fetch_Meta • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Get meta data from object
    
-    Source: R/Object_Utilities.R
+    Source: R/Generics.R, R/LIGER_Utilities.R, R/Object_Utilities.R
     
     
    
 
@@ -116,26 +122,30 @@ 
    Get meta data from object
    
     
    
 
     
    
-    
    Fetch_Meta(object)
+    
    Fetch_Meta(object, ...)
 
-# S3 method for Seurat
-Fetch_Meta(object)
+# S3 method for class 'liger'
+Fetch_Meta(object, ...)
 
-# S3 method for liger
-Fetch_Meta(object)
    
+# S3 method for class 'Seurat'
+Fetch_Meta(object, ...)
    
     
    
 
     
    
     
    Arguments
    
-    
    object
    
+
+
+
    object
    
 
    Object of class Seurat or liger.
    
 
+
+
    ...
    
+
    Arguments passed to other methods
    
+
 
    
     
    
     
    Value
    
-    
-
-
    A data.frame containing cell-level meta data
    
+    
    A data.frame containing cell-level meta data
    
     
    
 
     
    
@@ -170,15 +180,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Fetch_Meta.liger.html b/docs/reference/Fetch_Meta.liger.html
new file mode 100644
index 0000000000..918037aa65
--- /dev/null
+++ b/docs/reference/Fetch_Meta.liger.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Find_Factor_Cor.html b/docs/reference/Find_Factor_Cor.html
new file mode 100644
index 0000000000..3bd32b1aa0
--- /dev/null
+++ b/docs/reference/Find_Factor_Cor.html
@@ -0,0 +1,176 @@
+
+Find Factor Correlations — Find_Factor_Cor • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Find Factor Correlations
    
+    Source: R/LIGER_Utilities.R
+    
+    
    
+
+    
    
+    
    Calculate correlations between gene loadings for all factors in liger or Seurat object.
    
+    
    
+
+    
    
+    
    Find_Factor_Cor(object, reduction = NULL)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    object
    
+
    LIGER/Seurat object name.
    
+
+
+
    reduction
    
+
    reduction name to pull loadings for.  Only valid if supplying a Seurat object.
    
+
+
    
+    
    
+    
    Value
    
+    
    correlation matrix
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+factor_correlations <- Find_Factor_Cor(object = object)
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Gene_Present.html b/docs/reference/Gene_Present.html
index 177d0ebb94..b67f8ba727 100644
--- a/docs/reference/Gene_Present.html
+++ b/docs/reference/Gene_Present.html
@@ -1,213 +1,8 @@
-
-Check if genes/features are present   — Gene_Present • scCustomize
-    
-
-    
    
-      
    
-
-      
-
-      
    
-  
    
-    
    
-    
    Check if genes/features are present  [Soft-deprecated]
    
-    Source: R/Utilities.R
-    
-    
    
-
-    
    
-    
    Check if genes are present in object and return vector of found genes.  Return warning messages for
-genes not found.
    
-    
    
-
-    
    
-    
    Gene_Present(
-  data,
-  gene_list,
-  case_check = TRUE,
-  case_check_msg = TRUE,
-  print_msg = TRUE,
-  omit_warn = TRUE,
-  return_none = FALSE,
-  seurat_assay = NULL
-)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    data
    
-
    Name of input data.  Currently only data of classes: Seurat, liger, data.frame,
-dgCMatrix, dgTMatrix, tibble are accepted.  Gene_IDs must be present in rownames of the data.
    
-
-
-
    gene_list
    
-
    vector of genes to check.
    
-
-
-
    case_check
    
-
    logical. Whether or not to check if features are found if the case is changed from the
-input list (Sentence case to Upper and vice versa).  Default is TRUE.
    
-
-
-
    case_check_msg
    
-
    logical. Whether to print message to console if alternate case features are found
-in addition to inclusion in returned list.  Default is TRUE.
    
-
-
-
    print_msg
    
-
    logical. Whether message should be printed if all features are found.  Default is TRUE.
    
-
-
-
    omit_warn
    
-
    logical. Whether to print message about features that are not found in current object.
-Default is TRUE.
    
-
-
-
    return_none
    
-
    logical. Whether list of found vs. bad features should still be returned if no
-features are found.  Default is FALSE.
    
-
-
-
    seurat_assay
    
-
    Name of assay to pull feature names from if data is Seurat Object.
-Default is NULL which will check against features from all assays present.
    
-
-
    
-    
    
-    
    Value
    
-    
-
-
    A list of length 3 containing 1) found features, 2) not found features, 3) features found if
-case was modified.
    
-    
    
-
-    
    
-    
    Examples
    
-    
    if (FALSE) {
-features <- Gene_Present(data = obj_name, gene_list = DEG_list, print_msg = TRUE, case_check = TRUE)
-found_features <- features[[1]]
-}
-
-
    
-    
    
-  
    
-  
-
    
-
-
-      
    
-  
    Developed by Samuel Marsh.
    
-
    
-
-
    
-  
    Site built with pkgdown 2.0.7.
    
-
    
-
-      
    
-
-  
-
-
-  
-
-  
+
+  
+    
+    
+    
+  
+
 
diff --git a/docs/reference/Hue_Pal-1.png b/docs/reference/Hue_Pal-1.png
index 55eca44f2c..161e9af4c9 100644
Binary files a/docs/reference/Hue_Pal-1.png and b/docs/reference/Hue_Pal-1.png differ
diff --git a/docs/reference/Hue_Pal.html b/docs/reference/Hue_Pal.html
index 380c20e796..7b7790e395 100644
--- a/docs/reference/Hue_Pal.html
+++ b/docs/reference/Hue_Pal.html
@@ -1,9 +1,9 @@
 
-Hue_Pal — Hue_Pal • scCustomizeHue_Pal — Hue_Pal • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -121,15 +127,15 @@ 
    Hue_Pal
    
 
     
    
     
    Arguments
    
-    
    num_colors
    
+
+
+
    num_colors
    
 
    number of colors to return in palette.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    hue color palette (as many colors as desired)
    
+    
    hue color palette (as many colors as desired)
    
     
    
 
     
    
@@ -152,15 +158,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Idents.html b/docs/reference/Idents.html
new file mode 100644
index 0000000000..f17a93811b
--- /dev/null
+++ b/docs/reference/Idents.html
@@ -0,0 +1,196 @@
+
+Extract or set default identities from object — Idents.liger • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Extract or set default identities from object
    
+    Source: R/LIGER_Utilities.R
+    
+    
    
+
+    
    
+    
    Extract default identities from object in factor form.
    
+    
    
+
+    
    
+    
    # S3 method for class 'liger'
+Idents(object, ...)
+
+# S3 method for class 'liger'
+Idents(object, ...) <- value
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    object
    
+
    LIGER object name.
    
+
+
+
    ...
    
+
    Arguments passed to other methods
    
+
+
+
    value
    
+
    name of column in cellMeta slot to set as new default cluster/ident
    
+
+
    
+    
    
+    
    Value
    
+    
    factor
    
+
    object
    
+    
    
+    
    
+    
    Note
    
+    
    Use of Idents<- is only for setting new default ident/cluster from column already present in cellMeta.
+To add new column with new cluster values to cellMeta and set as default see Rename_Clusters.
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+# Extract idents
+object_idents <- Idents(object = liger_object)
+} # }
+
+if (FALSE) { # \dontrun{
+# Set idents
+Idents(object = liger_object) <- "new_annotation"
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Iterate_Barcode_Rank_Plot.html b/docs/reference/Iterate_Barcode_Rank_Plot.html
index 2a7478f11a..4c56fad543 100644
--- a/docs/reference/Iterate_Barcode_Rank_Plot.html
+++ b/docs/reference/Iterate_Barcode_Rank_Plot.html
@@ -1,9 +1,9 @@
 
-Iterative Barcode Rank Plots — Iterate_Barcode_Rank_Plot • scCustomizeIterative Barcode Rank Plots — Iterate_Barcode_Rank_Plot • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Iterative Barcode Rank Plots
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -134,74 +140,74 @@ 
    Iterative Barcode Rank Plots
    
 
     
    
     
    Arguments
    
-    
    dir_path_h5
    
+
+
+
    dir_path_h5
    
 
    path to parent directory (if multi_directory = TRUE) or directory containing
 all h5 files (if multi_directory = FALSE).
    
 
 
-
    multi_directory
    
+
    multi_directory
    
 
    logical, whether or not all h5 files are in their own subdirectories or in a
 single directory (default is TRUE; each in own subdirectory (e.g. output from Cell Ranger)).
    
 
 
-
    h5_filename
    
+
    h5_filename
    
 
    Either the file name of h5 file (if multi_directory = TRUE) or the shared
 suffix (if multi_directory = FALSE)
    
 
 
-
    cellranger_multi
    
+
    cellranger_multi
    
 
    logical, whether the outputs to be read are from Cell Ranger multi as opposed
 to Cell Ranger count (default is FALSE).  Only valid if multi_directory = FALSE.
    
 
 
-
    parallel
    
+
    parallel
    
 
    logical, should files be read in parallel (default is FALSE).
    
 
 
-
    num_cores
    
+
    num_cores
    
 
    Number of cores to use in parallel if parallel = TRUE.
    
 
 
-
    file_path
    
+
    file_path
    
 
    file path to use for saving PDF output.
    
 
 
-
    file_name
    
+
    file_name
    
 
    Name of PDF output file.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    point size for plotting, default is 6.
    
 
 
-
    raster_dpi
    
+
    raster_dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(1024, 1024).
    
 
 
-
    plateau
    
+
    plateau
    
 
    numerical values at which to add vertical line designating estimated
 empty droplet plateau (default is NULL).  Must be vector equal in length to number of samples.
    
 
 
-
    ...
    
+
    ...
    
 
    Additional parameters passed to Read10X_h5_Multi_Directory or Read10X_h5_GEO.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    pdf document
    
+    
    pdf document
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Iterate_Barcode_Rank_Plot(dir_path_h5 = "H5_PATH/", multi_directory = TRUE,
 h5_filename = "raw_feature_bc_matrix", parallel = TRUE, num_cores = 12, file_path = "OUTPUT_PATH",
 file_name = "Barcode_Rank_Plots")
-}
+} # }
 
 
    
     
    
@@ -217,15 +223,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Iterate_Cluster_Highlight_Plot.html b/docs/reference/Iterate_Cluster_Highlight_Plot.html
index 4a314ce128..9e957620a6 100644
--- a/docs/reference/Iterate_Cluster_Highlight_Plot.html
+++ b/docs/reference/Iterate_Cluster_Highlight_Plot.html
@@ -1,10 +1,10 @@
 
-Iterate Cluster Highlight Plot — Iterate_Cluster_Highlight_Plot • scCustomizeIterate Cluster Highlight Plot — Iterate_Cluster_Highlight_Plot • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Iterate Cluster Highlight Plot
    
-    Source: R/Seurat_Iterative_Plotting.R
+    Source: R/Plotting_Seurat_Iterative.R
     
     
    
 
@@ -136,70 +142,70 @@ 
    Iterate Cluster Highlight Plot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    highlight_color
    
+
    highlight_color
    
 
    Color to highlight cells (default "navy").  Can provide either single color to use for
 all clusters/plots or a vector of colors equal to the number of clusters to use (in order) for the clusters/plots.
    
 
 
-
    background_color
    
+
    background_color
    
 
    non-highlighted cell colors.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    point size for both highlighted cluster and background.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
 
 
-
    file_path
    
+
    file_path
    
 
    directory file path and/or file name prefix.  Defaults to current wd.
    
 
 
-
    file_name
    
+
    file_name
    
 
    name suffix to append after sample name.
    
 
 
-
    file_type
    
+
    file_type
    
 
    File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
    
 
 
-
    single_pdf
    
-
    saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf
    
+
    single_pdf
    
+
    saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf
    
 
 
-
    dpi
    
+
    dpi
    
 
    dpi for image saving.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed toDimPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Saved plots
    
+    
    Saved plots
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Iterate_Cluster_Highlight_Plot(seurat_object = object, highlight_color = "navy",
 background_color = "lightgray", file_path = "path/", file_name = "name", file_type = "pdf",
 single_pdf = TRUE)
-}
+} # }
 
 
    
     
    
@@ -215,15 +221,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Iterate_DimPlot_bySample.html b/docs/reference/Iterate_DimPlot_bySample.html
index eb4d2ed5bb..b6ddef7cd9 100644
--- a/docs/reference/Iterate_DimPlot_bySample.html
+++ b/docs/reference/Iterate_DimPlot_bySample.html
@@ -1,9 +1,9 @@
 
-Iterate DimPlot By Sample — Iterate_DimPlot_bySample • scCustomizeIterate DimPlot By Sample — Iterate_DimPlot_bySample • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Iterate DimPlot By Sample
    
-    Source: R/Seurat_Iterative_Plotting.R
+    Source: R/Plotting_Seurat_Iterative.R
     
     
    
 
@@ -137,81 +143,81 @@ 
    Iterate DimPlot By Sample
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    sample_column
    
+
    sample_column
    
 
    name of meta.data column containing sample names/ids (default is "orig.ident").
    
 
 
-
    file_path
    
+
    file_path
    
 
    directory file path and/or file name prefix.  Defaults to current wd.
    
 
 
-
    file_name
    
+
    file_name
    
 
    name suffix to append after sample name.
    
 
 
-
    file_type
    
+
    file_type
    
 
    File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
    
 
 
-
    single_pdf
    
-
    saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf
    
+
    single_pdf
    
+
    saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf
    
 
 
-
    dpi
    
+
    dpi
    
 
    dpi for image saving.
    
 
 
-
    color
    
+
    color
    
 
    color scheme to use.
    
 
 
-
    no_legend
    
+
    no_legend
    
 
    logical, whether or not to include plot legend, default is TRUE.
    
 
 
-
    title_prefix
    
+
    title_prefix
    
 
    Value that should be used for plot title prefix if no_legend = TRUE.
 If NULL the value of meta_data_column will be used.  Default is NULL.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (default is object default).
    
 
 
-
    dims
    
+
    dims
    
 
    Dimensions to plot.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to DimPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Iterate_DimPlot_bySample(seurat_object = object, file_path = "plots/", file_name = "tsne",
 file_type = ".jpg", dpi = 600, color = "black")
-}
+} # }
 
 
    
     
    
@@ -227,15 +233,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Iterate_FeaturePlot_scCustom.html b/docs/reference/Iterate_FeaturePlot_scCustom.html
index d0dc543082..23b3d307c6 100644
--- a/docs/reference/Iterate_FeaturePlot_scCustom.html
+++ b/docs/reference/Iterate_FeaturePlot_scCustom.html
@@ -1,9 +1,9 @@
 
-Iterative Plotting of Gene Lists using Custom FeaturePlots — Iterate_FeaturePlot_scCustom • scCustomizeIterative Plotting of Gene Lists using Custom FeaturePlots — Iterate_FeaturePlot_scCustom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Iterative Plotting of Gene Lists using Custom FeaturePlots
    
-    Source: R/Seurat_Iterative_Plotting.R
+    Source: R/Plotting_Seurat_Iterative.R
     
     
    
 
@@ -119,7 +125,6 @@ 
    Iterative Plotting of Gene Lists using Custom FeaturePlots
    
     
    Iterate_FeaturePlot_scCustom(
   seurat_object,
   features,
-  gene_list = deprecated(),
   colors_use = viridis_plasma_dark_high,
   na_color = "lightgray",
   na_cutoff = 1e-09,
@@ -145,118 +150,114 @@ 
    Iterative Plotting of Gene Lists using Custom FeaturePlots
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    features
    
+
    features
    
 
    vector of features to plot.  If a named vector is provided then the names for each gene
 will be incorporated into plot title if single_pdf = TRUE or into file name if FALSE.
    
 
 
-
    gene_list
    
-
    [Deprecated] soft-deprecated.  See features.
    
-
-
-
    colors_use
    
+
    colors_use
    
 
    color scheme to use.
    
 
 
-
    na_color
    
+
    na_color
    
 
    color for non-expressed cells.
    
 
 
-
    na_cutoff
    
+
    na_cutoff
    
 
    Value to use as minimum expression cutoff.  To set no cutoff set to NA.
    
 
 
-
    split.by
    
+
    split.by
    
 
    Variable in @meta.data to split the plot by.
    
 
 
-
    order
    
+
    order
    
 
    whether to move positive cells to the top (default = TRUE).
    
 
 
-
    return_plots
    
+
    return_plots
    
 
    logical. Whether to return plots to list instead of saving them to file(s).  Default is FALSE.
    
 
 
-
    file_path
    
+
    file_path
    
 
    directory file path and/or file name prefix.  Defaults to current wd.
    
 
 
-
    file_name
    
+
    file_name
    
 
    name suffix and file extension.
    
 
 
-
    file_type
    
+
    file_type
    
 
    File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
    
 
 
-
    single_pdf
    
+
    single_pdf
    
 
    saves all plots to single PDF file (default = FALSE).
    
 
 
-
    features_per_page
    
+
    features_per_page
    
 
    numeric, number of features to plot on single page if single_pdf = TRUE.  Default is 1.
    
 
 
-
    num_columns
    
+
    num_columns
    
 
    Number of columns in plot layout (only applicable if single_pdf = TRUE AND
 features_per_page > 1).
    
 
 
-
    landscape
    
+
    landscape
    
 
    logical, when plotting multiple features per page in single PDF whether to use landscape or portrait
 page dimensions (default is TRUE).
    
 
 
-
    dpi
    
+
    dpi
    
 
    dpi for image saving.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    alpha_exp
    
+
    alpha_exp
    
 
    new alpha level to apply to expressing cell color palette (colors_use).  Must be
 value between 0-1.
    
 
 
-
    alpha_na_exp
    
+
    alpha_na_exp
    
 
    new alpha level to apply to non-expressing cell color palette (na_color).  Must be
 value between 0-1.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to FeaturePlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Saved plots
    
+    
    Saved plots
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
-Iterate_FeaturePlot_scCustom(seurat_object = object, gene_list = DEG_list,
+    
    if (FALSE) { # \dontrun{
+Iterate_FeaturePlot_scCustom(seurat_object = object, features = DEG_list,
 colors_use = viridis_plasma_dark_high, na_color = "lightgray", file_path = "plots/",
 file_name = "tsne", file_type = ".jpg", dpi = 600)
-}
+} # }
 
 
    
     
    
@@ -272,15 +273,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Iterate_Meta_Highlight_Plot.html b/docs/reference/Iterate_Meta_Highlight_Plot.html
index 8c7c1f656a..224eeeb60a 100644
--- a/docs/reference/Iterate_Meta_Highlight_Plot.html
+++ b/docs/reference/Iterate_Meta_Highlight_Plot.html
@@ -1,9 +1,9 @@
 
-Iterate Meta Highlight Plot — Iterate_Meta_Highlight_Plot • scCustomizeIterate Meta Highlight Plot — Iterate_Meta_Highlight_Plot • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
     
    
     
    Iterate Meta Highlight Plot
    
-    Source: R/Seurat_Iterative_Plotting.R
+    Source: R/Plotting_Seurat_Iterative.R
     
     
    
 
@@ -139,92 +145,92 @@ 
    Iterate Meta Highlight Plot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    meta_data_column
    
+
    meta_data_column
    
 
    Name of the column in seurat_object@meta.data slot to pull value from for highlighting.
    
 
 
-
    new_meta_order
    
+
    new_meta_order
    
 
    The order in which to plot each level within meta_data_column if single_PDF is TRUE.
    
 
 
-
    meta_data_sort
    
+
    meta_data_sort
    
 
    logical.  Whether or not to sort and relevel the levels in meta_data_column if
 single_PDF is TRUE.  Default is TRUE.
    
 
 
-
    highlight_color
    
+
    highlight_color
    
 
    Color to highlight cells (default "navy").  Can provide either single color to use for
 all clusters/plots or a vector of colors equal to the number of clusters to use (in order) for the clusters/plots.
    
 
 
-
    background_color
    
+
    background_color
    
 
    non-highlighted cell colors.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    point size for both highlighted cluster and background.
    
 
 
-
    no_legend
    
+
    no_legend
    
 
    logical, whether or not to remove plot legend and move to plot title.  Default is FALSE.
    
 
 
-
    title_prefix
    
+
    title_prefix
    
 
    Value that should be used for plot title prefix if no_legend = TRUE.
 If NULL the value of meta_data_column will be used.  Default is NULL.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
 
 
-
    file_path
    
+
    file_path
    
 
    directory file path and/or file name prefix.  Defaults to current wd.
    
 
 
-
    file_name
    
+
    file_name
    
 
    name suffix to append after sample name.
    
 
 
-
    file_type
    
+
    file_type
    
 
    File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
    
 
 
-
    single_pdf
    
-
    saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf
    
+
    single_pdf
    
+
    saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf
    
 
 
-
    dpi
    
+
    dpi
    
 
    dpi for image saving.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed toDimPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Saved plots
    
+    
    Saved plots
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Iterate_Meta_Highlight_Plot(seurat_object = object, meta_data_column = "sample_id",
 highlight_color = "navy", background_color = "lightgray", file_path = "path/",
 file_name = "name", file_type = "pdf", single_pdf = TRUE)
-}
+} # }
 
 
    
     
    
@@ -240,15 +246,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Iterate_PC_Loading_Plots.html b/docs/reference/Iterate_PC_Loading_Plots.html
index 639e3bf6c6..b219b6f51b 100644
--- a/docs/reference/Iterate_PC_Loading_Plots.html
+++ b/docs/reference/Iterate_PC_Loading_Plots.html
@@ -1,9 +1,9 @@
 
-Iterate PC Loading Plots — Iterate_PC_Loading_Plots • scCustomizeIterate PC Loading Plots — Iterate_PC_Loading_Plots • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Iterate PC Loading Plots
    
-    Source: R/Seurat_Iterative_Plotting.R
+    Source: R/Plotting_Seurat_Iterative.R
     
     
    
 
@@ -128,36 +134,36 @@ 
    Iterate PC Loading Plots
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    dims_plot
    
+
    dims_plot
    
 
    number of PCs to plot (integer).  Default is all dims present in PCA.
    
 
 
-
    file_path
    
+
    file_path
    
 
    directory file path to save file.
    
 
 
-
    name_prefix
    
+
    name_prefix
    
 
    prefix for file name (optional).
    
 
 
-
    file_name
    
+
    file_name
    
 
    suffix for file name.  Default is "PC_Loading_Plots".
    
 
 
-
    return_plots
    
+
    return_plots
    
 
    Whether to return the plot list (Default is FALSE).  Must assign to environment
 to save plot list.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A list of plots outputted as pdf
    
+    
    A list of plots outputted as pdf
    
     
    
     
    
     
    See also
    
@@ -166,9 +172,9 @@ 
    See also
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Iterate_PC_Loading_Plots(seurat_object = seurat, dims_plot = 25, file_path = "plots/")
-}
+} # }
 
 
    
     
    
@@ -184,15 +190,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Iterate_Plot_Density_Custom.html b/docs/reference/Iterate_Plot_Density_Custom.html
index aa38752e81..8c8f1f4766 100644
--- a/docs/reference/Iterate_Plot_Density_Custom.html
+++ b/docs/reference/Iterate_Plot_Density_Custom.html
@@ -1,9 +1,9 @@
 
-Iterative Plotting of Gene Lists using Custom Density Plots — Iterate_Plot_Density_Custom • scCustomizeIterative Plotting of Gene Lists using Custom Density Plots — Iterate_Plot_Density_Custom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
     
    
     
    Iterative Plotting of Gene Lists using Custom Density Plots
    
-    Source: R/Seurat_Iterative_Plotting.R
+    Source: R/Plotting_Seurat_Iterative.R
     
     
    
 
@@ -136,76 +142,76 @@ 
    Iterative Plotting of Gene Lists using Custom Density Plots
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    gene_list
    
+
    gene_list
    
 
    vector of genes to plot.  If a named vector is provided then the names for each gene
 will be incorporated into plot title if single_pdf = TRUE or into file name if FALSE.
    
 
 
-
    viridis_palette
    
+
    viridis_palette
    
 
    color scheme to use.
    
 
 
-
    custom_palette
    
+
    custom_palette
    
 
    color for non-expressed cells.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    file_path
    
+
    file_path
    
 
    directory file path and/or file name prefix.  Defaults to current wd.
    
 
 
-
    file_name
    
+
    file_name
    
 
    name suffix and file extension.
    
 
 
-
    file_type
    
+
    file_type
    
 
    File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
    
 
 
-
    single_pdf
    
-
    saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.
    
+
    single_pdf
    
+
    saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf.
    
 
 
-
    dpi
    
+
    dpi
    
 
    dpi for image saving.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (if NULL then defaults to Object default)
    
 
 
-
    combine
    
+
    combine
    
 
    Create a single plot? If FALSE, a list with ggplot objects is returned.
    
 
 
-
    joint
    
+
    joint
    
 
    NULL.  This function only supports joint = FALSE.  Leave as NULL to generate plots.  To iterate joint plots see function: Iterate_Plot_Density_Joint.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to plot_density.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Saved plots
    
+    
    Saved plots
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Iterate_Plot_Density_Custom(seurat_object = object, gene_list = DEG_list, viridis_palette = "magma",
 file_path = "plots/", file_name = "_density_plots", file_type = ".jpg", dpi = 600)
-}
+} # }
 
 
    
     
    
@@ -221,15 +227,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Iterate_Plot_Density_Joint.html b/docs/reference/Iterate_Plot_Density_Joint.html
index d04b2674ce..7cbb20dc8f 100644
--- a/docs/reference/Iterate_Plot_Density_Joint.html
+++ b/docs/reference/Iterate_Plot_Density_Joint.html
@@ -1,9 +1,9 @@
 
-Iterative Plotting of Gene Lists using Custom Joint Density Plots — Iterate_Plot_Density_Joint • scCustomizeIterative Plotting of Gene Lists using Custom Joint Density Plots — Iterate_Plot_Density_Joint • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Iterative Plotting of Gene Lists using Custom Joint Density Plots
    
-    Source: R/Seurat_Iterative_Plotting.R
+    Source: R/Plotting_Seurat_Iterative.R
     
     
    
 
@@ -136,78 +142,78 @@ 
    Iterative Plotting of Gene Lists using Custom Joint Density Plots
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    gene_list
    
+
    gene_list
    
 
    a list of vectors of genes to plot jointly.  Each entry in the list will be plotted
 for the joint density.  All entries in list must be greater than 2 features.  If a named list is provided
 then the names for each list entry will be incorporated into plot title if single_pdf = TRUE or
 into file name if FALSE.
    
 
 
-
    viridis_palette
    
+
    viridis_palette
    
 
    color scheme to use.
    
 
 
-
    custom_palette
    
+
    custom_palette
    
 
    color for non-expressed cells.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    file_path
    
+
    file_path
    
 
    directory file path and/or file name prefix.  Defaults to current wd.
    
 
 
-
    file_name
    
+
    file_name
    
 
    name suffix and file extension.
    
 
 
-
    file_type
    
+
    file_type
    
 
    File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
    
 
 
-
    single_pdf
    
-
    saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.
    
+
    single_pdf
    
+
    saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf.
    
 
 
-
    dpi
    
+
    dpi
    
 
    dpi for image saving.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (if NULL then defaults to Object default)
    
 
 
-
    combine
    
+
    combine
    
 
    Create a single plot? If FALSE, a list with ggplot objects is returned.
    
 
 
-
    joint
    
+
    joint
    
 
    NULL.  This function only supports joint = FALSE.  Leave as NULL to generate plots.  To iterate joint plots see function: Iterate_Plot_Density_Joint.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to plot_density.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Saved plots
    
+    
    Saved plots
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Iterate_Plot_Density_Joint(seurat_object = object, gene_list = DEG_list, viridis_palette = "magma",
 file_path = "plots/", file_name = "joint_plots", file_type = ".jpg", dpi = 600)
-}
+} # }
 
 
    
     
    
@@ -223,15 +229,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Iterate_VlnPlot_scCustom.html b/docs/reference/Iterate_VlnPlot_scCustom.html
index 28f7ccc150..d10b8f3e19 100644
--- a/docs/reference/Iterate_VlnPlot_scCustom.html
+++ b/docs/reference/Iterate_VlnPlot_scCustom.html
@@ -1,9 +1,9 @@
 
-Iterative Plotting of Gene Lists using VlnPlot_scCustom — Iterate_VlnPlot_scCustom • scCustomizeIterative Plotting of Gene Lists using VlnPlot_scCustom — Iterate_VlnPlot_scCustom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Iterative Plotting of Gene Lists using VlnPlot_scCustom
    
-    Source: R/Seurat_Iterative_Plotting.R
+    Source: R/Plotting_Seurat_Iterative.R
     
     
    
 
@@ -119,7 +125,6 @@ 
    Iterative Plotting of Gene Lists using VlnPlot_scCustom
    
     
    Iterate_VlnPlot_scCustom(
   seurat_object,
   features,
-  gene_list = deprecated(),
   colors_use = NULL,
   pt.size = NULL,
   group.by = NULL,
@@ -138,89 +143,85 @@ 
    Iterative Plotting of Gene Lists using VlnPlot_scCustom
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
-
    Seurat object name.
    
 
 
-
    features
    
-
    vector of features to plot.
    
+
    seurat_object
    
+
    Seurat object name.
    
 
 
-
    gene_list
    
-
    [Deprecated] soft-deprecated.  See features.
    
+
    features
    
+
    vector of features to plot.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    color palette to use for plotting.  By default if number of levels plotted is less than
 or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE
 both from DiscretePalette_scCustomize.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    point size for plotting.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) plot by (for example, orig.ident);
 default is the current active.ident of the object.
    
 
 
-
    split.by
    
+
    split.by
    
 
    Feature to split plots by (i.e. "orig.ident").
    
 
 
-
    file_path
    
+
    file_path
    
 
    directory file path and/or file name prefix.  Defaults to current wd.
    
 
 
-
    file_name
    
+
    file_name
    
 
    name suffix and file extension.
    
 
 
-
    file_type
    
+
    file_type
    
 
    File type to save output as.  Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
    
 
 
-
    single_pdf
    
-
    saves all plots to single PDF file (default = FALSE).  `file_type`` must be .pdf.
    
+
    single_pdf
    
+
    saves all plots to single PDF file (default = FALSE).  `file_type“ must be .pdf.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).
    
 
 
-
    dpi
    
+
    dpi
    
 
    dpi for image saving.
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to VlnPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Saved plots
    
+    
    Saved plots
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
-Iterate_VlnPlot_scCustom(seurat_object = object, gene_list = DEG_list, colors = color_list,
+    
    if (FALSE) { # \dontrun{
+Iterate_VlnPlot_scCustom(seurat_object = object, features = DEG_list, colors = color_list,
 file_path = "plots/", file_name = "_vln", file_type = ".jpg", dpi = 600)
-}
+} # }
 
 
    
     
    
@@ -236,15 +237,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/JCO_Four-1.png b/docs/reference/JCO_Four-1.png
index af77213bdf..58b2d037a0 100644
Binary files a/docs/reference/JCO_Four-1.png and b/docs/reference/JCO_Four-1.png differ
diff --git a/docs/reference/JCO_Four.html b/docs/reference/JCO_Four.html
index 6f2cfd489b..69e87ff850 100644
--- a/docs/reference/JCO_Four.html
+++ b/docs/reference/JCO_Four.html
@@ -1,9 +1,9 @@
 
-Four Color Palette (JCO) — JCO_Four • scCustomizeFour Color Palette (JCO) — JCO_Four • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -121,9 +127,7 @@ 
    Four Color Palette (JCO)
    
 
     
    
     
    Value
    
-    
-
-
    4 color palette from the JCO ggsci palette
    
+    
    4 color palette from the JCO ggsci palette
    
     
    
     
    
     
    References
    
@@ -152,15 +156,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Liger_to_Seurat.html b/docs/reference/Liger_to_Seurat.html
index d53b770758..82a69cee18 100644
--- a/docs/reference/Liger_to_Seurat.html
+++ b/docs/reference/Liger_to_Seurat.html
@@ -1,10 +1,10 @@
 
-Create a Seurat object containing the data from a liger object  — Liger_to_Seurat • scCustomizeCreate a Seurat object containing the data from a liger object  — Liger_to_Seurat • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -136,68 +142,68 @@ 
    Create a Seurat object containing the data from a liger object 
     
    Arguments
    
-    
    liger_object
    
+
+
+
    liger_object
    
 
    liger object.
    
 
 
-
    nms
    
+
    nms
    
 
    By default, labels cell names with dataset of origin (this is to account for cells in
 different datasets which may have same name). Other names can be passed here as vector, must have
 same length as the number of datasets. (default names(H)).
    
 
 
-
    renormalize
    
+
    renormalize
    
 
    Whether to log-normalize raw data using Seurat defaults (default TRUE).
    
 
 
-
    use.liger.genes
    
+
    use.liger.genes
    
 
    Whether to carry over variable genes (default TRUE).
    
 
 
-
    by.dataset
    
+
    by.dataset
    
 
    Include dataset of origin in cluster identity in Seurat object (default FALSE).
    
 
 
-
    keep_meta
    
+
    keep_meta
    
 
    logical. Whether to transfer additional metadata (nGene/nUMI/dataset already transferred)
 to new Seurat Object.  Default is TRUE.
    
 
 
-
    reduction_label
    
+
    reduction_label
    
 
    Name of dimensionality reduction technique used.  Enables accurate transfer
 or name to Seurat object instead of defaulting to "tSNE".
    
 
 
-
    seurat_assay
    
+
    seurat_assay
    
 
    Name to set for assay in Seurat Object.  Default is "RNA".
    
 
 
-
    assay_type
    
+
    assay_type
    
 
    what type of Seurat assay to create in new object (Assay vs Assay5).
 Default is NULL which will default to the current user settings.
 See Convert_Assay parameter convert_to for acceptable values.
    
 
 
-
    add_barcode_names
    
+
    add_barcode_names
    
 
    logical, whether to add dataset names to the cell barcodes when
 creating Seurat object, default is FALSE.
    
 
 
-
    barcode_prefix
    
+
    barcode_prefix
    
 
    logical, if add_barcode_names = TRUE should the names be added as
 prefix to current cell barcodes/names or a suffix (default is TRUE; prefix).
    
 
 
-
    barcode_cell_id_delimiter
    
+
    barcode_cell_id_delimiter
    
 
    The delimiter to use when adding dataset id to barcode
 prefix/suffix.  Default is "_".
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Seurat object with raw.data, scale.data, reduction_label, iNMF, and ident slots set.
    
+    
    Seurat object with raw.data, scale.data, reduction_label, iNMF, and ident slots set.
    
     
    
     
    
     
    Details
    
@@ -213,9 +219,9 @@ 
    References
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 seurat_object <- Liger_to_Seurat(liger_object = LIGER_OBJ, reduction_label = "UMAP")
-}
+} # }
 
    
     
    
   
    
@@ -230,15 +236,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/MAD_Stats.html b/docs/reference/MAD_Stats.html
index 2ead22d2f9..41d0177ec2 100644
--- a/docs/reference/MAD_Stats.html
+++ b/docs/reference/MAD_Stats.html
@@ -1,9 +1,9 @@
 
-Median Absolute Deviation Statistics — MAD_Stats • scCustomizeMedian Absolute Deviation Statistics — MAD_Stats • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -127,42 +133,42 @@ 
    Median Absolute Deviation Statistics
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    group_by_var
    
+
    group_by_var
    
 
    Column in meta.data slot to group results by (default = "orig.ident").
    
 
 
-
    default_var
    
+
    default_var
    
 
    logical.  Whether to include the default meta.data variables of: "nCount_RNA",
 "nFeature_RNA", "percent_mito", "percent_ribo", "percent_mito_ribo", and "log10GenesPerUMI"
 in addition to variables supplied to mad_var.
    
 
 
-
    mad_var
    
+
    mad_var
    
 
    Column(s) in @meta.data to calculate medians for in addition to defaults.
 Must be of class() integer or numeric.
    
 
 
-
    mad_num
    
+
    mad_num
    
 
    integer value to multiply the MAD in returned data.frame (default is 2).
 Often helpful when calculating a outlier range to base of of median + (X*MAD).
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A data.frame.
    
+    
    A data.frame.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 mad_stats <- MAD_Stats(seurat_object = obj, group_by_var = "orig.ident")
-}
+} # }
 
 
    
     
    
@@ -178,15 +184,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Median_Stats.html b/docs/reference/Median_Stats.html
index 6e2ac12830..5cb68dba2e 100644
--- a/docs/reference/Median_Stats.html
+++ b/docs/reference/Median_Stats.html
@@ -1,9 +1,9 @@
 
-Median Statistics — Median_Stats • scCustomizeMedian Statistics — Median_Stats • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -126,37 +132,37 @@ 
    Median Statistics
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    group_by_var
    
+
    group_by_var
    
 
    Column in meta.data slot to group results by (default = "orig.ident").
    
 
 
-
    default_var
    
+
    default_var
    
 
    logical.  Whether to include the default meta.data variables of: "nCount_RNA",
 "nFeature_RNA", "percent_mito", "percent_ribo", "percent_mito_ribo", and "log10GenesPerUMI"
 in addition to variables supplied to median_var.
    
 
 
-
    median_var
    
+
    median_var
    
 
    Column(s) in @meta.data to calculate medians for in addition to defaults.
 Must be of class() integer or numeric.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A data.frame.
    
+    
    A data.frame.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 med_stats <- Median_Stats(seurat_object - obj, group_by_var = "orig.ident")
-}
+} # }
 
 
    
     
    
@@ -172,15 +178,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Merge_Seurat_List.html b/docs/reference/Merge_Seurat_List.html
index 2b26f010a3..e2d944c25c 100644
--- a/docs/reference/Merge_Seurat_List.html
+++ b/docs/reference/Merge_Seurat_List.html
@@ -1,9 +1,9 @@
 
-Merge a list of Seurat Objects — Merge_Seurat_List • scCustomizeMerge a list of Seurat Objects — Merge_Seurat_List • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -112,7 +118,7 @@ 
    Merge a list of Seurat Objects
    
     
    
 
     
    
-    
    Enables easy merge of a list of Seurat Objects.  See  See merge for more information,
    
+    
    Enables easy merge of a list of Seurat Objects.  See  See merge for more information,
    
     
    
 
     
    
@@ -126,38 +132,38 @@ 
    Merge a list of Seurat Objects
    
 
     
    
     
    Arguments
    
-    
    list_seurat
    
+
+
+
    list_seurat
    
 
    list composed of multiple Seurat Objects.
    
 
 
-
    add.cell.ids
    
+
    add.cell.ids
    
 
    A character vector of equal length to the number of objects in list_seurat.
-Appends the corresponding values to the start of each objects' cell names.  See merge.
    
+Appends the corresponding values to the start of each objects' cell names.  See merge.
    
 
 
-
    merge.data
    
+
    merge.data
    
 
    Merge the data slots instead of just merging the counts (which requires renormalization).
 This is recommended if the same normalization approach was applied to all objects.
-See merge.
    
+See merge.
    
 
 
-
    project
    
-
    Project name for the Seurat object. See merge.
    
+
    project
    
+
    Project name for the Seurat object. See merge.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A Seurat Object
    
+    
    A Seurat Object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 object_list <- list(obj1, obj2, obj3, ...)
 merged_object <- Merge_Seurat_List(list_seurat = object_list)
-}
+} # }
 
 
    
     
    
@@ -173,15 +179,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Merge_Sparse_Data_All.html b/docs/reference/Merge_Sparse_Data_All.html
index fd0e6adbf4..33ff2a7ae7 100644
--- a/docs/reference/Merge_Sparse_Data_All.html
+++ b/docs/reference/Merge_Sparse_Data_All.html
@@ -1,9 +1,9 @@
 
-Merge a list of Sparse Matrices — Merge_Sparse_Data_All • scCustomizeMerge a list of Sparse Matrices — Merge_Sparse_Data_All • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -126,43 +132,43 @@ 
    Merge a list of Sparse Matrices
    
 
     
    
     
    Arguments
    
-    
    matrix_list
    
+
+
+
    matrix_list
    
 
    list of matrices to merge.
    
 
 
-
    add_cell_ids
    
+
    add_cell_ids
    
 
    a vector of sample ids to add as prefix to cell barcode during merge.
    
 
 
-
    prefix
    
+
    prefix
    
 
    logical.  Whether add_cell_ids should be added as prefix to current cell barcodes/names
 or as suffix to current cell barcodes/names.  Default is TRUE, add as prefix.
    
 
 
-
    cell_id_delimiter
    
+
    cell_id_delimiter
    
 
    The delimiter to use when adding cell id prefix/suffix.  Default is "_".
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A sparse Matrix
    
+    
    A sparse Matrix
    
     
    
     
    
     
    References
    
-    
    Original function is part of LIGER package as non-exported function
-https://github.com/welch-lab/liger/blob/master/R/utilities.R (License: GPL-3).
+    
    Original function is part of LIGER package
+https://github.com/welch-lab/liger/blob/master/R/mergeObject.R (License: GPL-3).
 Function was modified for use in scCustomize (add progress bar, prefix vs. suffix, and delimiter options).
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data_list <- Read10X_GEO(...)
 merged <- Merge_Sparse_Data_All(matrix_list = data_list, add_cell_ids = names(data_list),
 prefix = TRUE, cell_id_delimiter = "_")
-}
+} # }
 
 
    
     
    
@@ -178,15 +184,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Merge_Sparse_Multimodal_All.html b/docs/reference/Merge_Sparse_Multimodal_All.html
index 122700d469..d37e4929b6 100644
--- a/docs/reference/Merge_Sparse_Multimodal_All.html
+++ b/docs/reference/Merge_Sparse_Multimodal_All.html
@@ -1,9 +1,9 @@
 
-Merge a list of Sparse Matrices contain multi-modal data. — Merge_Sparse_Multimodal_All • scCustomizeMerge a list of Sparse Matrices contain multi-modal data. — Merge_Sparse_Multimodal_All • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -126,37 +132,37 @@ 
    Merge a list of Sparse Matrices contain multi-modal data.
    
 
     
    
     
    Arguments
    
-    
    matrix_list
    
+
+
+
    matrix_list
    
 
    list of matrices to merge.
    
 
 
-
    add_cell_ids
    
+
    add_cell_ids
    
 
    a vector of sample ids to add as prefix to cell barcode during merge.
    
 
 
-
    prefix
    
+
    prefix
    
 
    logical.  Whether add_cell_ids should be added as prefix to current cell barcodes/names
 or as suffix to current cell barcodes/names.  Default is TRUE, add as prefix.
    
 
 
-
    cell_id_delimiter
    
+
    cell_id_delimiter
    
 
    The delimiter to use when adding cell id prefix/suffix.  Default is "_".
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A list containing one sparse matrix for each modality
    
+    
    A list containing one sparse matrix for each modality
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data_list <- Read10X_GEO(...)
 merged_list <- Merge_Sparse_Multimodal_All(matrix_list = data_list, add_cell_ids = names(data_list),
 prefix = TRUE, cell_id_delimiter = "_")
-}
+} # }
 
 
    
     
    
@@ -172,15 +178,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Meta_Highlight_Plot-1.png b/docs/reference/Meta_Highlight_Plot-1.png
index fb485f46e8..c0975ba1ef 100644
Binary files a/docs/reference/Meta_Highlight_Plot-1.png and b/docs/reference/Meta_Highlight_Plot-1.png differ
diff --git a/docs/reference/Meta_Highlight_Plot.html b/docs/reference/Meta_Highlight_Plot.html
index 2e405e3c72..a76fc7be34 100644
--- a/docs/reference/Meta_Highlight_Plot.html
+++ b/docs/reference/Meta_Highlight_Plot.html
@@ -1,9 +1,9 @@
 
-Meta Highlight Plot — Meta_Highlight_Plot • scCustomizeMeta Highlight Plot — Meta_Highlight_Plot • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Meta Highlight Plot
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -130,6 +136,7 @@ 
    Meta Highlight Plot
    
   label = FALSE,
   split.by = NULL,
   split_seurat = FALSE,
+  reduction = NULL,
   ggplot_default_colors = FALSE,
   ...
 )
    
@@ -137,77 +144,81 @@ 
    Meta Highlight Plot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    meta_data_column
    
+
    meta_data_column
    
 
    Name of the column in seurat_object@meta.data slot to pull value from for highlighting.
    
 
 
-
    meta_data_highlight
    
+
    meta_data_highlight
    
 
    Name of variable(s) within meta_data_name to highlight in the plot.
    
 
 
-
    highlight_color
    
+
    highlight_color
    
 
    Color to highlight cells (default "navy").
    
 
 
-
    background_color
    
+
    background_color
    
 
    non-highlighted cell colors.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    point size for both highlighted cluster and background.
    
 
 
-
    aspect_ratio
    
+
    aspect_ratio
    
 
    Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.
    
 
 
-
    figure_plot
    
+
    figure_plot
    
 
    logical.  Whether to remove the axes and plot with legend on left of plot denoting
 axes labels.  (Default is FALSE).  Requires split_seurat = TRUE.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    label
    
+
    label
    
 
    Whether to label the highlighted meta data variable(s).  Default is FALSE.
    
 
 
-
    split.by
    
+
    split.by
    
 
    Variable in @meta.data to split the plot by.
    
 
 
-
    split_seurat
    
+
    split_seurat
    
 
    logical.  Whether or not to display split plots like Seurat (shared y axis) or as
 individual plots in layout.  Default is FALSE.
    
 
 
-
    ggplot_default_colors
    
+
    reduction
    
+
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
+
+
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed toDimPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -234,15 +245,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Meta_Numeric.html b/docs/reference/Meta_Numeric.html
index 419b65973d..5e0fe90b89 100644
--- a/docs/reference/Meta_Numeric.html
+++ b/docs/reference/Meta_Numeric.html
@@ -1,10 +1,10 @@
 
-Check if meta data columns are numeric — Meta_Numeric • scCustomizeCheck if meta data columns are numeric — Meta_Numeric • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -123,22 +129,22 @@ 
    Check if meta data columns are numeric
    
 
     
    
     
    Arguments
    
-    
    data
    
+
+
+
    data
    
 
    a data.frame contain meta.data.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    vector of meta data columns that are numeric.
    
+    
    vector of meta data columns that are numeric.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 numeric_meta_columns <- Meta_Numeric(data = meta_data)
-}
+} # }
 
 
    
     
    
@@ -154,15 +160,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Meta_Present.html b/docs/reference/Meta_Present.html
index 45c7680272..3448efa0f7 100644
--- a/docs/reference/Meta_Present.html
+++ b/docs/reference/Meta_Present.html
@@ -1,10 +1,10 @@
 
-Check if meta data are present — Meta_Present • scCustomizeCheck if meta data are present — Meta_Present • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -120,7 +126,6 @@ 
    Check if meta data are present
    
     
    
     
    Meta_Present(
   object,
-  seurat_object = deprecated(),
   meta_col_names,
   print_msg = TRUE,
   omit_warn = TRUE,
@@ -130,43 +135,39 @@ 
    Check if meta data are present
    
 
     
    
     
    Arguments
    
-    
    object
    
-
    Seurat or Liger object name.
    
 
 
-
    seurat_object
    
-
    [Deprecated] deprecated.  Please use object instead.
    
+
    object
    
+
    Seurat or Liger object name.
    
 
 
-
    meta_col_names
    
+
    meta_col_names
    
 
    vector of column names to check.
    
 
 
-
    print_msg
    
+
    print_msg
    
 
    logical. Whether message should be printed if all features are found.  Default is TRUE.
    
 
 
-
    omit_warn
    
+
    omit_warn
    
 
    logical. Whether to print message about features that are not found in current object. Default is TRUE.
    
 
 
-
    return_none
    
+
    return_none
    
 
    logical. Whether list of found vs. bad features should still be returned if no
 meta_col_names are found.  Default is FALSE.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    vector of meta data columns that are present
    
+    
    vector of meta data columns that are present
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 meta_variables <- Meta_Present(object = obj_name, meta_col_names = "percent_mito", print_msg = TRUE)
-}
+} # }
 
 
    
     
    
@@ -182,15 +183,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Meta_Present_LIGER.html b/docs/reference/Meta_Present_LIGER.html
index a4f3ae918c..b67f8ba727 100644
--- a/docs/reference/Meta_Present_LIGER.html
+++ b/docs/reference/Meta_Present_LIGER.html
@@ -1,177 +1,8 @@
-
-Check if meta data are present — Meta_Present_LIGER • scCustomize
-    
-
-    
    
-      
    
-
-      
-
-      
    
-  
    
-    
    
-    
    Check if meta data are present
    
-    Source: R/LIGER_Utilities.R
-    
-    
    
-
-    
    
-    
    Check if meta data columns are present in object and return vector of found columns  Return warning
-messages for meta data columns not found.
    
-    
    
-
-    
    
-    
    Meta_Present_LIGER(liger_object, meta_col_names, print_msg = TRUE)
    
-    
    
-
-    
    
-    
    Arguments
    
-    
    liger_object
    
-
    object name.
    
-
-
-
    meta_col_names
    
-
    vector of column names to check.
    
-
-
-
    print_msg
    
-
    logical. Whether message should be printed if all features are found.  Default is TRUE.
    
-
-
    
-    
    
-    
    Value
    
-    
-
-
    vector of meta data columns that are present
    
-    
    
-
-    
    
-    
    Examples
    
-    
    if (FALSE) {
-meta_variables <- Meta_Present_LIGER(liger_object = obj, meta_col_names = DEG_list,
-print_msg = TRUE)
-}
-
-
    
-    
    
-  
    
-  
-
    
-
-
-      
    
-  
    Developed by Samuel Marsh.
    
-
    
-
-
    
-  
    Site built with pkgdown 2.0.7.
    
-
    
-
-      
    
-
-  
-
-
-  
-
-  
+
+  
+    
+    
+    
+  
+
 
diff --git a/docs/reference/Meta_Remove_Seurat.html b/docs/reference/Meta_Remove_Seurat.html
index b4840682bb..f938523793 100644
--- a/docs/reference/Meta_Remove_Seurat.html
+++ b/docs/reference/Meta_Remove_Seurat.html
@@ -1,9 +1,9 @@
 
-Remove meta data columns containing Seurat Defaults — Meta_Remove_Seurat • scCustomizeRemove meta data columns containing Seurat Defaults — Meta_Remove_Seurat • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -126,36 +132,36 @@ 
    Remove meta data columns containing Seurat Defaults
    
 
     
    
     
    Arguments
    
-    
    meta_data
    
+
+
+
    meta_data
    
 
    data.frame containing meta data.
    
 
 
-
    seurat_object
    
+
    seurat_object
    
 
    object name.
    
 
 
-
    barcodes_to_rownames
    
+
    barcodes_to_rownames
    
 
    logical, are barcodes present as column and should they be moved to
-rownames (to be compatible with Seurat::AddMetaData).  Default is FALSE.
    
+rownames (to be compatible with Seurat::AddMetaData).  Default is FALSE.
    
 
 
-
    barcodes_colname
    
+
    barcodes_colname
    
 
    name of barcodes column in meta_data.  Required if barcodes_to_rownames = TRUE.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    data.frame with only new columns.
    
+    
    data.frame with only new columns.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 new_meta <- Meta_Remove_Seurat(meta_data = meta_data_df, seurat_object = object)
-object <- AddMetaData(object = object, metadata = new_meta)
-}
+object <- AddMetaData(object = object, metadata = new_meta)
+} # }
 
 
    
     
    
@@ -171,15 +177,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Move_Legend-1.png b/docs/reference/Move_Legend-1.png
index b8fd49aa07..3934f6bf87 100644
Binary files a/docs/reference/Move_Legend-1.png and b/docs/reference/Move_Legend-1.png differ
diff --git a/docs/reference/Move_Legend.html b/docs/reference/Move_Legend.html
index e821b6fe7e..6918c1f458 100644
--- a/docs/reference/Move_Legend.html
+++ b/docs/reference/Move_Legend.html
@@ -1,9 +1,9 @@
 
-Move Legend Position — Move_Legend • scCustomizeMove Legend Position — Move_Legend • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -121,19 +127,19 @@ 
    Move Legend Position
    
 
     
    
     
    Arguments
    
-    
    position
    
+
+
+
    position
    
 
    valid position to move legend.  Default is "right".
    
 
 
-
    ...
    
+
    ...
    
 
    extra arguments passed to ggplot2::theme().
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Returns a list-like object of class theme.
    
+    
    Returns a list-like object of class theme.
    
     
    
 
     
    
@@ -159,15 +165,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/NavyAndOrange-1.png b/docs/reference/NavyAndOrange-1.png
index 0acd7b123b..4c01cb1575 100644
Binary files a/docs/reference/NavyAndOrange-1.png and b/docs/reference/NavyAndOrange-1.png differ
diff --git a/docs/reference/NavyAndOrange.html b/docs/reference/NavyAndOrange.html
index 80441407d2..6675595b4f 100644
--- a/docs/reference/NavyAndOrange.html
+++ b/docs/reference/NavyAndOrange.html
@@ -1,9 +1,9 @@
 
-Navy and Orange Dual Color Palette — NavyAndOrange • scCustomizeNavy and Orange Dual Color Palette — NavyAndOrange • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,15 +127,15 @@ 
    Navy and Orange Dual Color Palette
    
 
     
    
     
    Arguments
    
-    
    flip_order
    
+
+
+
    flip_order
    
 
    Whether to flip the order of colors.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Navy orange palette
    
+    
    Navy orange palette
    
     
    
 
     
    
@@ -152,15 +158,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/PC_Plotting-1.png b/docs/reference/PC_Plotting-1.png
index 90fd067a6e..a454162fe0 100644
Binary files a/docs/reference/PC_Plotting-1.png and b/docs/reference/PC_Plotting-1.png differ
diff --git a/docs/reference/PC_Plotting.html b/docs/reference/PC_Plotting.html
index 453f17c7be..1015dce85b 100644
--- a/docs/reference/PC_Plotting.html
+++ b/docs/reference/PC_Plotting.html
@@ -1,10 +1,10 @@
 
-PC Plots — PC_Plotting • scCustomizePC Plots — PC_Plotting • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -123,19 +129,19 @@ 
    PC Plots
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat Object.
    
 
 
-
    dim_number
    
+
    dim_number
    
 
    A single dim to plot (integer).
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A plot of PC heatmap and gene loadings for single
    
+    
    A plot of PC heatmap and gene loadings for single
    
     
    
     
    
     
    See also
    
@@ -165,15 +171,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/PalettePlot-1.png b/docs/reference/PalettePlot-1.png
index 1c1f7ad7f0..d9ed012b42 100644
Binary files a/docs/reference/PalettePlot-1.png and b/docs/reference/PalettePlot-1.png differ
diff --git a/docs/reference/PalettePlot.html b/docs/reference/PalettePlot.html
index 0d39292da0..ab977253ee 100644
--- a/docs/reference/PalettePlot.html
+++ b/docs/reference/PalettePlot.html
@@ -1,9 +1,9 @@
 
-Plot color palette in viewer — PalettePlot • scCustomizePlot color palette in viewer — PalettePlot • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,20 +127,20 @@ 
    Plot color palette in viewer
    
 
     
    
     
    Arguments
    
-    
    pal
    
+
+
+
    pal
    
 
    a vector of colors (either named colors of hex codes).
    
 
 
-
    label_color_num
    
+
    label_color_num
    
 
    logical, whether or not to numerically label the colors in output plot.
 Default is TRUE is number of colors in pal is less than 75 and FALSE is greater than 75.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Plot of all colors in supplied palette/vector
    
+    
    Plot of all colors in supplied palette/vector
    
     
    
     
    
     
    References
    
@@ -162,15 +168,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Percent_Expressing.html b/docs/reference/Percent_Expressing.html
index 1dc4b5a1ee..8828299bb2 100644
--- a/docs/reference/Percent_Expressing.html
+++ b/docs/reference/Percent_Expressing.html
@@ -1,9 +1,9 @@
 
-Calculate percent of expressing cells — Percent_Expressing • scCustomizeCalculate percent of expressing cells — Percent_Expressing • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -123,7 +129,6 @@ 
    Calculate percent of expressing cells
    
   group_by = NULL,
   split_by = NULL,
   entire_object = FALSE,
-  slot = deprecated(),
   layer = "data",
   assay = NULL
 )
    
@@ -131,48 +136,44 @@ 
    Calculate percent of expressing cells
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    features
    
+
    features
    
 
    Feature(s) to plot.
    
 
 
-
    threshold
    
+
    threshold
    
 
    Expression threshold to use for calculation of percent expressing (default is 0).
    
 
 
-
    group_by
    
+
    group_by
    
 
    Factor to group the cells by.
    
 
 
-
    split_by
    
+
    split_by
    
 
    Factor to split the groups by.
    
 
 
-
    entire_object
    
+
    entire_object
    
 
    logical (default = FALSE).  Whether to calculate percent of expressing cells
 across the entire object as opposed to by cluster or by group_by variable.
    
 
 
-
    slot
    
-
    [Deprecated] soft-deprecated.  See layer
    
-
-
-
    layer
    
+
    layer
    
 
    Which layer to pull expression data from?  Default is "data".
    
 
 
-
    assay
    
+
    assay
    
 
    Assay to pull feature data from.  Default is active assay.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A data.frame
    
+    
    A data.frame
    
     
    
     
    
     
    References
    
@@ -183,9 +184,9 @@ 
    References
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 percent_stats <- Percent_Expressing(seurat_object = object, features = "Cx3cr1", threshold = 0)
-}
+} # }
 
 
    
     
    
@@ -201,15 +202,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Plot_Cells_per_Sample.html b/docs/reference/Plot_Cells_per_Sample.html
index e0c3b5bed7..1027ad6903 100644
--- a/docs/reference/Plot_Cells_per_Sample.html
+++ b/docs/reference/Plot_Cells_per_Sample.html
@@ -1,9 +1,9 @@
 
-Plot Number of Cells/Nuclei per Sample — Plot_Cells_per_Sample • scCustomizePlot Number of Cells/Nuclei per Sample — Plot_Cells_per_Sample • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Plot Number of Cells/Nuclei per Sample
    
-    Source: R/Statistics_Plotting.R
+    Source: R/Plotting_Statistics.R
     
     
    
 
@@ -133,63 +139,63 @@ 
    Plot Number of Cells/Nuclei per Sample
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    sample_col
    
+
    sample_col
    
 
    Specify which column in meta.data specifies sample ID (i.e. orig.ident).
    
 
 
-
    group_by
    
+
    group_by
    
 
    Column in meta.data slot to group results by (i.e. "Treatment").
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    List of colors or color palette to use.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if group_by is not NULL.  Default is 1.
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Plot title.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    legend_title
    
+
    legend_title
    
 
    Label for plot legend.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Plot_Cells_per_Sample(seurat_object = obj, sample_col = "orig.ident", group_by = "Treatment")
-}
+} # }
 
 
    
     
    
@@ -205,15 +211,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Plot_Density_Custom.html b/docs/reference/Plot_Density_Custom.html
index 7e3f24cbdc..e183a34dbb 100644
--- a/docs/reference/Plot_Density_Custom.html
+++ b/docs/reference/Plot_Density_Custom.html
@@ -1,9 +1,9 @@
 
-Nebulosa Density Plot — Plot_Density_Custom • scCustomizeNebulosa Density Plot — Plot_Density_Custom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Nebulosa Density Plot
    
-    Source: R/Nebulosa_Plotting.R
+    Source: R/Plotting_Nebulosa.R
     
     
    
 
@@ -132,61 +138,61 @@ 
    Nebulosa Density Plot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    features
    
+
    features
    
 
    Features to plot.
    
 
 
-
    joint
    
+
    joint
    
 
    logical. Whether to return joint density plot. Default is FALSE.
    
 
 
-
    viridis_palette
    
+
    viridis_palette
    
 
    default viridis palette to use (must be one of: "viridis", "magma", "cividis",
 "inferno", "plasma").  Default is "magma".
    
 
 
-
    custom_palette
    
+
    custom_palette
    
 
    non-default color palette to be used in place of default viridis options.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    aspect_ratio
    
+
    aspect_ratio
    
 
    Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
 
 
-
    combine
    
+
    combine
    
 
    Create a single plot? If FALSE, a list with ggplot objects is returned.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to plot_density.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 library(Seurat)
 Plot_Density_Custom(seurat_object = pbmc_small, features = "CD3E")
-}
+} # }
 
 
    
     
    
@@ -202,15 +208,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Plot_Density_Joint_Only.html b/docs/reference/Plot_Density_Joint_Only.html
index 3a3615b59e..749f49d252 100644
--- a/docs/reference/Plot_Density_Joint_Only.html
+++ b/docs/reference/Plot_Density_Joint_Only.html
@@ -1,9 +1,9 @@
 
-Nebulosa Joint Density Plot — Plot_Density_Joint_Only • scCustomizeNebulosa Joint Density Plot — Plot_Density_Joint_Only • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Nebulosa Joint Density Plot
    
-    Source: R/Nebulosa_Plotting.R
+    Source: R/Plotting_Nebulosa.R
     
     
    
 
@@ -130,53 +136,53 @@ 
    Nebulosa Joint Density Plot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    features
    
+
    features
    
 
    Features to plot.
    
 
 
-
    viridis_palette
    
+
    viridis_palette
    
 
    default viridis palette to use (must be one of: "viridis", "magma", "cividis",
 "inferno", "plasma").  Default is "magma".
    
 
 
-
    custom_palette
    
+
    custom_palette
    
 
    non-default color palette to be used in place of default viridis options.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    aspect_ratio
    
+
    aspect_ratio
    
 
    Control the aspect ratio (y:x axes ratio length).  Must be numeric value;
 Default is NULL.
    
 
 
-
    reduction
    
+
    reduction
    
 
    Dimensionality Reduction to use (if NULL then defaults to Object default).
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to plot_density.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 library(Seurat)
 Plot_Density_Joint_Only(seurat_object = pbmc_small, features = c("CD8A", "CD3E"))
-}
+} # }
 
 
    
     
    
@@ -192,15 +198,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Plot_Median_Genes-1.png b/docs/reference/Plot_Median_Genes-1.png
index 0c7ec99fc2..2d1aed29e1 100644
Binary files a/docs/reference/Plot_Median_Genes-1.png and b/docs/reference/Plot_Median_Genes-1.png differ
diff --git a/docs/reference/Plot_Median_Genes.html b/docs/reference/Plot_Median_Genes.html
index 1646af34de..28f700d562 100644
--- a/docs/reference/Plot_Median_Genes.html
+++ b/docs/reference/Plot_Median_Genes.html
@@ -1,9 +1,9 @@
 
-Plot Median Genes per Cell per Sample — Plot_Median_Genes • scCustomizePlot Median Genes per Cell per Sample — Plot_Median_Genes • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Plot Median Genes per Cell per Sample
    
-    Source: R/Statistics_Plotting.R
+    Source: R/Plotting_Statistics.R
     
     
    
 
@@ -133,56 +139,56 @@ 
    Plot Median Genes per Cell per Sample
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    sample_col
    
+
    sample_col
    
 
    Specify which column in meta.data specifies sample ID (i.e. orig.ident).
    
 
 
-
    group_by
    
+
    group_by
    
 
    Column in meta.data slot to group results by (i.e. "Treatment").
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    List of colors or color palette to use.  Only applicable if group_by is not NULL.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if group_by is not NULL.  Default is 1.
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Plot title.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    legend_title
    
+
    legend_title
    
 
    Label for plot legend.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -211,15 +217,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Plot_Median_Mito.html b/docs/reference/Plot_Median_Mito.html
index bf9a72f095..cdfaabeeef 100644
--- a/docs/reference/Plot_Median_Mito.html
+++ b/docs/reference/Plot_Median_Mito.html
@@ -1,9 +1,9 @@
 
-Plot Median Percent Mito per Cell per Sample — Plot_Median_Mito • scCustomizePlot Median Percent Mito per Cell per Sample — Plot_Median_Mito • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Plot Median Percent Mito per Cell per Sample
    
-    Source: R/Statistics_Plotting.R
+    Source: R/Plotting_Statistics.R
     
     
    
 
@@ -133,67 +139,67 @@ 
    Plot Median Percent Mito per Cell per Sample
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    sample_col
    
+
    sample_col
    
 
    Specify which column in meta.data specifies sample ID (i.e. orig.ident).
    
 
 
-
    group_by
    
+
    group_by
    
 
    Column in meta.data slot to group results by (i.e. "Treatment").
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    List of colors or color palette to use.  Only applicable if group_by is not NULL.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if group_by is not NULL.  Default is 1.
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Plot title.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    legend_title
    
+
    legend_title
    
 
    Label for plot legend.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # Add mito
 obj <- Add_Mito_Ribo_Seurat(seurat_object = obj, species = "human")
 
 # Plot
 Plot_Median_Mito(seurat_object = obj, sample_col = "orig.ident",  group_by = "sample_id")
-}
+} # }
 
 
    
     
    
@@ -209,15 +215,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Plot_Median_Other.html b/docs/reference/Plot_Median_Other.html
index 7e15ed516c..041e9884a1 100644
--- a/docs/reference/Plot_Median_Other.html
+++ b/docs/reference/Plot_Median_Other.html
@@ -1,9 +1,9 @@
 
-Plot Median other variable per Cell per Sample — Plot_Median_Other • scCustomizePlot Median other variable per Cell per Sample — Plot_Median_Other • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Plot Median other variable per Cell per Sample
    
-    Source: R/Statistics_Plotting.R
+    Source: R/Plotting_Statistics.R
     
     
    
 
@@ -134,65 +140,65 @@ 
    Plot Median other variable per Cell per Sample
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    median_var
    
+
    median_var
    
 
    Variable in meta.data slot to calculate and plot median values for.
    
 
 
-
    sample_col
    
+
    sample_col
    
 
    Specify which column in meta.data specifies sample ID (i.e. orig.ident).
    
 
 
-
    group_by
    
+
    group_by
    
 
    Column in meta.data slot to group results by (i.e. "Treatment").
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    List of colors or color palette to use.  Only applicable if group_by is not NULL.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if group_by is not NULL.  Default is 1.
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Plot title.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    legend_title
    
+
    legend_title
    
 
    Label for plot legend.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 library(Seurat)
 cd_features <- list(c('CD79B', 'CD79A', 'CD19', 'CD180', 'CD200', 'CD3D', 'CD2','CD3E',
 'CD7','CD8A', 'CD14', 'CD1C', 'CD68', 'CD9', 'CD247'))
@@ -202,7 +208,7 @@ 
    Examples
    
 
 Plot_Median_Other(seurat_object = pbmc_small, median_var = "CD_Features1",
 sample_col = "orig.ident", group_by = "Treatment")
-}
+} # }
 
 
    
     
    
@@ -218,15 +224,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Plot_Median_UMIs-1.png b/docs/reference/Plot_Median_UMIs-1.png
index 27d11a4fab..1a1a5b5806 100644
Binary files a/docs/reference/Plot_Median_UMIs-1.png and b/docs/reference/Plot_Median_UMIs-1.png differ
diff --git a/docs/reference/Plot_Median_UMIs.html b/docs/reference/Plot_Median_UMIs.html
index 75d1752cd6..6f2d584716 100644
--- a/docs/reference/Plot_Median_UMIs.html
+++ b/docs/reference/Plot_Median_UMIs.html
@@ -1,9 +1,9 @@
 
-Plot Median UMIs per Cell per Sample — Plot_Median_UMIs • scCustomizePlot Median UMIs per Cell per Sample — Plot_Median_UMIs • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Plot Median UMIs per Cell per Sample
    
-    Source: R/Statistics_Plotting.R
+    Source: R/Plotting_Statistics.R
     
     
    
 
@@ -133,56 +139,56 @@ 
    Plot Median UMIs per Cell per Sample
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    sample_col
    
+
    sample_col
    
 
    Specify which column in meta.data specifies sample ID (i.e. orig.ident).
    
 
 
-
    group_by
    
+
    group_by
    
 
    Column in meta.data slot to group results by (i.e. "Treatment").
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    List of colors or color palette to use.  Only applicable if group_by is not NULL.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if group_by is not NULL.  Default is 1.
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Plot title.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    legend_title
    
+
    legend_title
    
 
    Label for plot legend.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -211,15 +217,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Proportion_Plot-1.png b/docs/reference/Proportion_Plot-1.png
new file mode 100644
index 0000000000..704c893cea
Binary files /dev/null and b/docs/reference/Proportion_Plot-1.png differ
diff --git a/docs/reference/Proportion_Plot.html b/docs/reference/Proportion_Plot.html
new file mode 100644
index 0000000000..4d074aabd5
--- /dev/null
+++ b/docs/reference/Proportion_Plot.html
@@ -0,0 +1,225 @@
+
+Cell Proportion Plot — Proportion_Plot • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Cell Proportion Plot
    
+    Source: R/Plotting_Statistics.R
+    
+    
    
+
+    
    
+    
    Plots the proportion of cells belonging to each identity in active.ident of Seurat object.
+Can plot either the totals or split by a variable in meta.data.
    
+    
    
+
+    
    
+    
    Proportion_Plot(
+  seurat_object,
+  plot_type = "bar",
+  plot_scale = "percent",
+  group_by_var = "ident",
+  split.by = NULL,
+  num_columns = NULL,
+  x_lab_rotate = FALSE,
+  colors_use = NULL,
+  ggplot_default_colors = FALSE,
+  color_seed = 123
+)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    seurat_object
    
+
    Seurat object name.
    
+
+
+
    plot_type
    
+
    whether to plot a pie chart or bar chart; value must be one of "bar" or "pie". Default
+is "bar"
    
+
+
+
    plot_scale
    
+
    whether to plot bar chart as total cell counts or percents, value must be one of "percent" or
+"count". Default is "percent".
    
+
+
+
    group_by_var
    
+
    meta data column to classify samples (default = "ident" and will use active.ident.
    
+
+
+
    split.by
    
+
    meta data variable to use to split plots.  Default is NULL which will plot across entire object.
    
+
+
+
    num_columns
    
+
    number of columns in plot.  Only valid if split.by is not NULL.
    
+
+
+
    x_lab_rotate
    
+
    Rotate x-axis labels 45 degrees (Default is FALSE). Only valid if plot_type = "bar".
    
+
+
+
    colors_use
    
+
    color palette to use for plotting.
    
+
+
+
    ggplot_default_colors
    
+
    logical.  If colors_use = NULL, Whether or not to return plot using
+default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
+
+
+
    color_seed
    
+
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
+groups plotted is greater than 36.  Default = 123.
    
+
+
    
+    
    
+    
    Value
    
+    
    ggplot2 or patchwork object
    
+    
    
+
+    
    
+    
    Examples
    
+    
    #' library(Seurat)
+Proportion_Plot(seurat_object = pbmc_small)
+
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Pull_Cluster_Annotation.html b/docs/reference/Pull_Cluster_Annotation.html
index 66edb243b2..947242190a 100644
--- a/docs/reference/Pull_Cluster_Annotation.html
+++ b/docs/reference/Pull_Cluster_Annotation.html
@@ -1,10 +1,10 @@
 
-Pull cluster information from annotation csv file. — Pull_Cluster_Annotation • scCustomizePull cluster information from annotation csv file. — Pull_Cluster_Annotation • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -127,29 +133,29 @@ 
    Pull cluster information from annotation csv file.
    
 
     
    
     
    Arguments
    
-    
    annotation
    
+
+
+
    annotation
    
 
    name of the data.frame/tibble or path to CSV file containing cluster annotation.
    
 
 
-
    cluster_name_col
    
+
    cluster_name_col
    
 
    name of column containing cluster names/numbers (default is "cluster").
    
 
 
-
    cell_type_col
    
+
    cell_type_col
    
 
    name of column contain the cell type annotation (default is "cell_type").
    
 
 
    
     
    
     
    Value
    
-    
-
-
    a list of named vectors for every cell type in the cell_type_col column of the annotation table and
+    
    a list of named vectors for every cell type in the cell_type_col column of the annotation table and
 vectors new cluster names (for use with Rename_Clusters function or manual identity renaming).
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # If pulling from a data.frame/tibble
 cluster_annotation <- Pull_Cluster_Annotation(annotation = annotation_df,
 cluster_name_col = "cluster", cell_type_col = "cell_type")
@@ -157,7 +163,7 @@ 
    Examples
    
 # If pulling from csv file
 cluster_annotation <- Pull_Cluster_Annotation(annotation = "file_path/file_name.csv",
 cluster_name_col = "cluster", cell_type_col = "cell_type")
-}
+} # }
 
 
    
     
    
@@ -173,15 +179,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Pull_Directory_List.html b/docs/reference/Pull_Directory_List.html
index 77a1fb6986..46a6309fe1 100644
--- a/docs/reference/Pull_Directory_List.html
+++ b/docs/reference/Pull_Directory_List.html
@@ -1,9 +1,9 @@
 
-Pull Directory List — Pull_Directory_List • scCustomizePull Directory List — Pull_Directory_List • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,23 +127,23 @@ 
    Pull Directory List
    
 
     
    
     
    Arguments
    
-    
    base_path
    
+
+
+
    base_path
    
 
    path to the parent directory which contains all of the subdirectories of interest.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A vector of sub-directories within base_path.
    
+    
    A vector of sub-directories within base_path.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data_dir <- 'path/to/data/directory'
 library_list <- Pull_Directory_List(base_path = data_dir)
-}
+} # }
 
 
    
     
    
@@ -153,15 +159,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/QC_Histogram.html b/docs/reference/QC_Histogram.html
index d8e228d029..df8ed3e5c4 100644
--- a/docs/reference/QC_Histogram.html
+++ b/docs/reference/QC_Histogram.html
@@ -1,9 +1,9 @@
 
-QC Histogram Plots — QC_Histogram • scCustomizeQC Histogram Plots — QC_Histogram • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Histogram Plots
    
-    Source: R/QC_Plotting_Seurat.R
+    Source: R/Plotting_QC_Seurat.R
     
     
    
 
@@ -121,6 +127,7 @@ 
    QC Histogram Plots
    
   features,
   low_cutoff = NULL,
   high_cutoff = NULL,
+  cutoff_line_width = NULL,
   split.by = NULL,
   bins = 250,
   colors_use = "dodgerblue",
@@ -133,64 +140,68 @@ 
    QC Histogram Plots
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    features
    
+
    features
    
 
    Feature from meta.data, assay features, or feature name shortcut to plot.
    
 
 
-
    low_cutoff
    
+
    low_cutoff
    
 
    Plot line a potential low threshold for filtering.
    
 
 
-
    high_cutoff
    
+
    high_cutoff
    
 
    Plot line a potential high threshold for filtering.
    
 
 
-
    split.by
    
+
    cutoff_line_width
    
+
    numerical value for thickness of cutoff lines, default is NULL.
    
+
+
+
    split.by
    
 
    Feature to split plots by (i.e. "orig.ident").
    
 
 
-
    bins
    
+
    bins
    
 
    number of bins to plot default is 250.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    color to fill histogram bars, default is "dodgerblue".
    
 
 
-
    num_columns
    
+
    num_columns
    
 
    Number of columns in plot layout.
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    optional, vector to use for plot title.  Default is the name of the
 variable being plotted.
    
 
 
-
    assay
    
+
    assay
    
 
    assay to pull features from, default is active assay.
    
 
 
-
    print_defaults
    
+
    print_defaults
    
 
    return list of accepted default shortcuts to provide to features instead
 of full name.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A patchwork object
    
+    
    A patchwork object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 QC_Histogram(seurat_object = object, features = "nFeature_RNA")
-}
+} # }
 
 
    
     
    
@@ -206,15 +217,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/QC_Plot_GenevsFeature.html b/docs/reference/QC_Plot_GenevsFeature.html
index 357b494f54..a65dfce001 100644
--- a/docs/reference/QC_Plot_GenevsFeature.html
+++ b/docs/reference/QC_Plot_GenevsFeature.html
@@ -1,9 +1,9 @@
 
-QC Plots Genes vs Misc — QC_Plot_GenevsFeature • scCustomizeQC Plots Genes vs Misc — QC_Plot_GenevsFeature • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Genes vs Misc
    
-    Source: R/QC_Plotting_Seurat.R
+    Source: R/Plotting_QC_Seurat.R
     
     
    
 
@@ -125,6 +131,7 @@ 
    QC Plots Genes vs Misc
    
   high_cutoff_gene = NULL,
   low_cutoff_feature = NULL,
   high_cutoff_feature = NULL,
+  cutoff_line_width = NULL,
   colors_use = NULL,
   pt.size = 1,
   group.by = NULL,
@@ -139,91 +146,95 @@ 
    QC Plots Genes vs Misc
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    feature1
    
+
    feature1
    
 
    First feature to plot.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    low_cutoff_gene
    
+
    low_cutoff_gene
    
 
    Plot line a potential low threshold for filtering genes per cell.
    
 
 
-
    high_cutoff_gene
    
+
    high_cutoff_gene
    
 
    Plot line a potential high threshold for filtering genes per cell.
    
 
 
-
    low_cutoff_feature
    
+
    low_cutoff_feature
    
 
    Plot line a potential low threshold for filtering feature1 per cell.
    
 
 
-
    high_cutoff_feature
    
+
    high_cutoff_feature
    
 
    Plot line a potential high threshold for filtering feature1 per cell.
    
 
 
-
    colors_use
    
+
    cutoff_line_width
    
+
    numerical value for thickness of cutoff lines, default is NULL.
    
+
+
+
    colors_use
    
 
    vector of colors to use for plotting by identity.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident).
 Default is @active.ident.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if greater
 than 100,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using default
 ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    shuffle_seed
    
+
    shuffle_seed
    
 
    Sets the seed if randomly shuffling the order of points (Default is 1).
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to FeatureScatter.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 QC_Plot_GenevsFeature(seurat_object = obj, y_axis_label = "Feature per Cell")
-}
+} # }
 
 
    
     
    
@@ -239,15 +250,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/QC_Plot_UMIvsFeature.html b/docs/reference/QC_Plot_UMIvsFeature.html
index 9d3de6311d..8bbf46b8ce 100644
--- a/docs/reference/QC_Plot_UMIvsFeature.html
+++ b/docs/reference/QC_Plot_UMIvsFeature.html
@@ -1,9 +1,9 @@
 
-QC Plots UMI vs Misc — QC_Plot_UMIvsFeature • scCustomizeQC Plots UMI vs Misc — QC_Plot_UMIvsFeature • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots UMI vs Misc
    
-    Source: R/QC_Plotting_Seurat.R
+    Source: R/Plotting_QC_Seurat.R
     
     
    
 
@@ -125,6 +131,7 @@ 
    QC Plots UMI vs Misc
    
   high_cutoff_UMI = NULL,
   low_cutoff_feature = NULL,
   high_cutoff_feature = NULL,
+  cutoff_line_width = NULL,
   colors_use = NULL,
   pt.size = 1,
   group.by = NULL,
@@ -139,91 +146,95 @@ 
    QC Plots UMI vs Misc
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    feature1
    
+
    feature1
    
 
    First feature to plot.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    low_cutoff_UMI
    
+
    low_cutoff_UMI
    
 
    Plot line a potential low threshold for filtering UMI per cell.
    
 
 
-
    high_cutoff_UMI
    
+
    high_cutoff_UMI
    
 
    Plot line a potential high threshold for filtering UMI per cell.
    
 
 
-
    low_cutoff_feature
    
+
    low_cutoff_feature
    
 
    Plot line a potential low threshold for filtering feature1 per cell.
    
 
 
-
    high_cutoff_feature
    
+
    high_cutoff_feature
    
 
    Plot line a potential high threshold for filtering feature1 per cell.
    
 
 
-
    colors_use
    
+
    cutoff_line_width
    
+
    numerical value for thickness of cutoff lines, default is NULL.
    
+
+
+
    colors_use
    
 
    vector of colors to use for plotting by identity.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident).
 Default is @active.ident.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if greater
 than 100,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    shuffle_seed
    
+
    shuffle_seed
    
 
    Sets the seed if randomly shuffling the order of points (Default is 1).
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to FeatureScatter.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 QC_Plot_UMIvsFeature(seurat_object = obj, y_axis_label = "Feature per Cell")
-}
+} # }
 
 
    
     
    
@@ -239,15 +250,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/QC_Plot_UMIvsGene-1.png b/docs/reference/QC_Plot_UMIvsGene-1.png
index a0f3cb0e52..9e9eed3041 100644
Binary files a/docs/reference/QC_Plot_UMIvsGene-1.png and b/docs/reference/QC_Plot_UMIvsGene-1.png differ
diff --git a/docs/reference/QC_Plot_UMIvsGene.html b/docs/reference/QC_Plot_UMIvsGene.html
index 48cd9eb400..8acc79d753 100644
--- a/docs/reference/QC_Plot_UMIvsGene.html
+++ b/docs/reference/QC_Plot_UMIvsGene.html
@@ -1,9 +1,9 @@
 
-QC Plots Genes vs UMIs — QC_Plot_UMIvsGene • scCustomizeQC Plots Genes vs UMIs — QC_Plot_UMIvsGene • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Genes vs UMIs
    
-    Source: R/QC_Plotting_Seurat.R
+    Source: R/Plotting_QC_Seurat.R
     
     
    
 
@@ -124,6 +130,7 @@ 
    QC Plots Genes vs UMIs
    
   high_cutoff_gene = Inf,
   low_cutoff_UMI = -Inf,
   high_cutoff_UMI = Inf,
+  cutoff_line_width = NULL,
   colors_use = NULL,
   meta_gradient_name = NULL,
   meta_gradient_color = viridis_plasma_dark_high,
@@ -145,114 +152,118 @@ 
    QC Plots Genes vs UMIs
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    low_cutoff_gene
    
+
    low_cutoff_gene
    
 
    Plot line a potential low threshold for filtering genes per cell.
    
 
 
-
    high_cutoff_gene
    
+
    high_cutoff_gene
    
 
    Plot line a potential high threshold for filtering genes per cell.
    
 
 
-
    low_cutoff_UMI
    
+
    low_cutoff_UMI
    
 
    Plot line a potential low threshold for filtering UMIs per cell.
    
 
 
-
    high_cutoff_UMI
    
+
    high_cutoff_UMI
    
 
    Plot line a potential high threshold for filtering UMIs per cell.
    
 
 
-
    colors_use
    
+
    cutoff_line_width
    
+
    numerical value for thickness of cutoff lines, default is NULL.
    
+
+
+
    colors_use
    
 
    vector of colors to use for plotting by identity.
    
 
 
-
    meta_gradient_name
    
+
    meta_gradient_name
    
 
    Name of continuous meta data variable to color points in plot by.
 (MUST be continuous variable i.e. "percent_mito").
    
 
 
-
    meta_gradient_color
    
+
    meta_gradient_color
    
 
    The gradient color palette to use for plotting of meta variable (default is
 viridis "Plasma" palette with dark colors high).
    
 
 
-
    meta_gradient_na_color
    
+
    meta_gradient_na_color
    
 
    Color to use for plotting values when a meta_gradient_low_cutoff is
 set (default is "lightgray").
    
 
 
-
    meta_gradient_low_cutoff
    
+
    meta_gradient_low_cutoff
    
 
    Value to use as threshold for plotting.  meta_gradient_name values
 below this value will be plotted using meta_gradient_na_color.
    
 
 
-
    cells
    
+
    cells
    
 
    Cells to include on the scatter plot (default is all cells).
    
 
 
-
    combination
    
+
    combination
    
 
    logical (default FALSE).  Whether or not to return a plot layout with both the
 plot colored by identity and the meta data gradient plot.
    
 
 
-
    ident_legend
    
+
    ident_legend
    
 
    logical, whether to plot the legend containing identities (left plot) when
 combination = TRUE.  Default is TRUE.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Passes size of points to both FeatureScatter and geom_point.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident).
 Default is @active.ident.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    Random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    shuffle_seed
    
+
    shuffle_seed
    
 
    Sets the seed if randomly shuffling the order of points (Default is 1).
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to FeatureScatter.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -276,15 +287,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/QC_Plots_Combined_Vln.html b/docs/reference/QC_Plots_Combined_Vln.html
index 2348f14f35..379d6f4ffb 100644
--- a/docs/reference/QC_Plots_Combined_Vln.html
+++ b/docs/reference/QC_Plots_Combined_Vln.html
@@ -1,9 +1,9 @@
 
-QC Plots Genes, UMIs, & % Mito — QC_Plots_Combined_Vln • scCustomizeQC Plots Genes, UMIs, & % Mito — QC_Plots_Combined_Vln • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Genes, UMIs, & % Mito
    
-    Source: R/QC_Plotting_Seurat.R
+    Source: R/Plotting_QC_Seurat.R
     
     
    
 
@@ -123,6 +129,7 @@ 
    QC Plots Genes, UMIs, & % Mito
    
   UMI_cutoffs = NULL,
   mito_cutoffs = NULL,
   mito_name = "percent_mito",
+  cutoff_line_width = NULL,
   pt.size = NULL,
   plot_median = FALSE,
   median_size = 15,
@@ -139,91 +146,95 @@ 
    QC Plots Genes, UMIs, & % Mito
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.
    
 
 
-
    feature_cutoffs
    
+
    feature_cutoffs
    
 
    Numeric vector of length 1 or 2 to plot lines for  potential low/high threshold for filtering.
    
 
 
-
    UMI_cutoffs
    
+
    UMI_cutoffs
    
 
    Numeric vector of length 1 or 2 to plot lines for  potential low/high threshold for filtering.
    
 
 
-
    mito_cutoffs
    
+
    mito_cutoffs
    
 
    Numeric vector of length 1 or 2 to plot lines for  potential low/high threshold for filtering.
    
 
 
-
    mito_name
    
+
    mito_name
    
 
    The column name containing percent mitochondrial counts information.  Default value is
-"percent_mito" which is default value created when using Add_Mito_Ribo_Seurat().
    
+"percent_mito" which is default value created when using Add_Mito_Ribo().
    
+
+
+
    cutoff_line_width
    
+
    numerical value for thickness of cutoff lines, default is NULL.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Point size for plotting
    
 
 
-
    plot_median
    
+
    plot_median
    
 
    logical, whether to plot median for each ident on the plot (Default is FALSE).
    
 
 
-
    median_size
    
+
    median_size
    
 
    Shape size for the median is plotted.
    
 
 
-
    plot_boxplot
    
+
    plot_boxplot
    
 
    logical, whether to plot boxplot inside of violin (Default is FALSE).
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    vector of colors to use for plot.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    Rotate x-axis labels 45 degrees (Default is TRUE).
    
 
 
-
    y_axis_log
    
+
    y_axis_log
    
 
    logical. Whether to change y axis to log10 scale (Default is FALSE).
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to VlnPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 QC_Plots_Combined_Vln(seurat_object = object)
-}
+} # }
 
 
    
     
    
@@ -239,15 +250,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/QC_Plots_Complexity-1.png b/docs/reference/QC_Plots_Complexity-1.png
index 657d3e9506..0ea93a9ca9 100644
Binary files a/docs/reference/QC_Plots_Complexity-1.png and b/docs/reference/QC_Plots_Complexity-1.png differ
diff --git a/docs/reference/QC_Plots_Complexity.html b/docs/reference/QC_Plots_Complexity.html
index 451a2d60db..38f90027e9 100644
--- a/docs/reference/QC_Plots_Complexity.html
+++ b/docs/reference/QC_Plots_Complexity.html
@@ -1,9 +1,9 @@
 
-QC Plots Cell "Complexity" — QC_Plots_Complexity • scCustomizeQC Plots Cell "Complexity" — QC_Plots_Complexity • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Cell "Complexity"
    
-    Source: R/QC_Plotting_Seurat.R
+    Source: R/Plotting_QC_Seurat.R
     
     
    
 
@@ -125,6 +131,7 @@ 
    QC Plots Cell "Complexity"
    
   plot_title = "Cell Complexity",
   low_cutoff = NULL,
   high_cutoff = NULL,
+  cutoff_line_width = NULL,
   pt.size = NULL,
   plot_median = FALSE,
   plot_boxplot = FALSE,
@@ -141,91 +148,95 @@ 
    QC Plots Cell "Complexity"
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    feature
    
+
    feature
    
 
    Feature from Meta Data to plot.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Plot Title.
    
 
 
-
    low_cutoff
    
+
    low_cutoff
    
 
    Plot line a potential low threshold for filtering.
    
 
 
-
    high_cutoff
    
+
    high_cutoff
    
 
    Plot line a potential high threshold for filtering.
    
 
 
-
    pt.size
    
+
    cutoff_line_width
    
+
    numerical value for thickness of cutoff lines, default is NULL.
    
+
+
+
    pt.size
    
 
    Point size for plotting
    
 
 
-
    plot_median
    
+
    plot_median
    
 
    logical, whether to plot median for each ident on the plot (Default is FALSE).
    
 
 
-
    plot_boxplot
    
+
    plot_boxplot
    
 
    logical, whether to plot boxplot inside of violin (Default is FALSE).
    
 
 
-
    median_size
    
+
    median_size
    
 
    Shape size for the median is plotted.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    vector of colors to use for plot.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    Rotate x-axis labels 45 degrees (Default is TRUE).
    
 
 
-
    y_axis_log
    
+
    y_axis_log
    
 
    logical. Whether to change y axis to log10 scale (Default is FALSE).
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to VlnPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -250,15 +261,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/QC_Plots_Feature.html b/docs/reference/QC_Plots_Feature.html
index e42797aea5..b9e1bd23f3 100644
--- a/docs/reference/QC_Plots_Feature.html
+++ b/docs/reference/QC_Plots_Feature.html
@@ -1,9 +1,9 @@
 
-QC Plots Feature — QC_Plots_Feature • scCustomizeQC Plots Feature — QC_Plots_Feature • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Feature
    
-    Source: R/QC_Plotting_Seurat.R
+    Source: R/Plotting_QC_Seurat.R
     
     
    
 
@@ -125,6 +131,7 @@ 
    QC Plots Feature
    
   plot_title = NULL,
   low_cutoff = NULL,
   high_cutoff = NULL,
+  cutoff_line_width = NULL,
   pt.size = NULL,
   plot_median = FALSE,
   median_size = 15,
@@ -141,100 +148,104 @@ 
    QC Plots Feature
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    feature
    
+
    feature
    
 
    Feature from Meta Data to plot.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Plot Title.
    
 
 
-
    low_cutoff
    
+
    low_cutoff
    
 
    Plot line a potential low threshold for filtering.
    
 
 
-
    high_cutoff
    
+
    high_cutoff
    
 
    Plot line a potential high threshold for filtering.
    
 
 
-
    pt.size
    
+
    cutoff_line_width
    
+
    numerical value for thickness of cutoff lines, default is NULL.
    
+
+
+
    pt.size
    
 
    Point size for plotting.
    
 
 
-
    plot_median
    
+
    plot_median
    
 
    logical, whether to plot median for each ident on the plot (Default is FALSE).
    
 
 
-
    median_size
    
+
    median_size
    
 
    Shape size for the median is plotted.
    
 
 
-
    plot_boxplot
    
+
    plot_boxplot
    
 
    logical, whether to plot boxplot inside of violin (Default is FALSE).
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    vector of colors to use for plot.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    Rotate x-axis labels 45 degrees (Default is TRUE).
    
 
 
-
    y_axis_log
    
+
    y_axis_log
    
 
    logical. Whether to change y axis to log10 scale (Default is FALSE).
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to VlnPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 QC_Plots_Feature(seurat_object = object, feature = "FEATURE_NAME",
 y_axis_label = "FEATURE per Cell", plot_title = "FEATURE per Cell", high_cutoff = 10,
 low_cutoff = 2)
-}
+} # }
 
 
    
     
    
@@ -250,15 +261,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/QC_Plots_Genes-1.png b/docs/reference/QC_Plots_Genes-1.png
index 456a3df624..b85fcb3bd4 100644
Binary files a/docs/reference/QC_Plots_Genes-1.png and b/docs/reference/QC_Plots_Genes-1.png differ
diff --git a/docs/reference/QC_Plots_Genes.html b/docs/reference/QC_Plots_Genes.html
index 949455e632..6366302e36 100644
--- a/docs/reference/QC_Plots_Genes.html
+++ b/docs/reference/QC_Plots_Genes.html
@@ -1,9 +1,9 @@
 
-QC Plots Genes — QC_Plots_Genes • scCustomizeQC Plots Genes — QC_Plots_Genes • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Genes
    
-    Source: R/QC_Plotting_Seurat.R
+    Source: R/Plotting_QC_Seurat.R
     
     
    
 
@@ -124,6 +130,7 @@ 
    QC Plots Genes
    
   y_axis_label = "Features",
   low_cutoff = NULL,
   high_cutoff = NULL,
+  cutoff_line_width = NULL,
   pt.size = NULL,
   plot_median = FALSE,
   plot_boxplot = FALSE,
@@ -140,87 +147,91 @@ 
    QC Plots Genes
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Plot Title.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    low_cutoff
    
+
    low_cutoff
    
 
    Plot line a potential low threshold for filtering.
    
 
 
-
    high_cutoff
    
+
    high_cutoff
    
 
    Plot line a potential high threshold for filtering.
    
 
 
-
    pt.size
    
+
    cutoff_line_width
    
+
    numerical value for thickness of cutoff lines, default is NULL.
    
+
+
+
    pt.size
    
 
    Point size for plotting.
    
 
 
-
    plot_median
    
+
    plot_median
    
 
    logical, whether to plot median for each ident on the plot (Default is FALSE).
    
 
 
-
    plot_boxplot
    
+
    plot_boxplot
    
 
    logical, whether to plot boxplot inside of violin (Default is FALSE).
    
 
 
-
    median_size
    
+
    median_size
    
 
    Shape size for the median is plotted.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    vector of colors to use for plot.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    Rotate x-axis labels 45 degrees (Default is TRUE).
    
 
 
-
    y_axis_log
    
+
    y_axis_log
    
 
    logical. Whether to change y axis to log10 scale (Default is FALSE).
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to VlnPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -244,15 +255,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/QC_Plots_Mito.html b/docs/reference/QC_Plots_Mito.html
index 34c4288083..bb3c2a8bd3 100644
--- a/docs/reference/QC_Plots_Mito.html
+++ b/docs/reference/QC_Plots_Mito.html
@@ -1,9 +1,9 @@
 
-QC Plots Mito — QC_Plots_Mito • scCustomizeQC Plots Mito — QC_Plots_Mito • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Mito
    
-    Source: R/QC_Plotting_Seurat.R
+    Source: R/Plotting_QC_Seurat.R
     
     
    
 
@@ -125,6 +131,7 @@ 
    QC Plots Mito
    
   y_axis_label = "% Mitochondrial Gene Counts",
   low_cutoff = NULL,
   high_cutoff = NULL,
+  cutoff_line_width = NULL,
   pt.size = NULL,
   plot_median = FALSE,
   median_size = 15,
@@ -141,99 +148,103 @@ 
    QC Plots Mito
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    mito_name
    
+
    mito_name
    
 
    The column name containing percent mitochondrial counts information.  Default value is
-"percent_mito" which is default value created when using Add_Mito_Ribo_Seurat().
    
+"percent_mito" which is default value created when using Add_Mito_Ribo().
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Plot Title.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    low_cutoff
    
+
    low_cutoff
    
 
    Plot line a potential low threshold for filtering.
    
 
 
-
    high_cutoff
    
+
    high_cutoff
    
 
    Plot line a potential high threshold for filtering.
    
 
 
-
    pt.size
    
+
    cutoff_line_width
    
+
    numerical value for thickness of cutoff lines, default is NULL.
    
+
+
+
    pt.size
    
 
    Point size for plotting.
    
 
 
-
    plot_median
    
+
    plot_median
    
 
    logical, whether to plot median for each ident on the plot (Default is FALSE).
    
 
 
-
    median_size
    
+
    median_size
    
 
    Shape size for the median is plotted.
    
 
 
-
    plot_boxplot
    
+
    plot_boxplot
    
 
    logical, whether to plot boxplot inside of violin (Default is FALSE).
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    vector of colors to use for plot.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    Rotate x-axis labels 45 degrees (Default is TRUE).
    
 
 
-
    y_axis_log
    
+
    y_axis_log
    
 
    logical. Whether to change y axis to log10 scale (Default is FALSE).
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to VlnPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 QC_Plots_Mito(seurat_object = object, plot_title = "Percent Mito per Cell", high_cutoff = 10)
-}
+} # }
 
 
    
     
    
@@ -249,15 +260,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/QC_Plots_UMIs-1.png b/docs/reference/QC_Plots_UMIs-1.png
index ebc7928464..9af94e23da 100644
Binary files a/docs/reference/QC_Plots_UMIs-1.png and b/docs/reference/QC_Plots_UMIs-1.png differ
diff --git a/docs/reference/QC_Plots_UMIs.html b/docs/reference/QC_Plots_UMIs.html
index 47c47fc2b4..339bc3bd8c 100644
--- a/docs/reference/QC_Plots_UMIs.html
+++ b/docs/reference/QC_Plots_UMIs.html
@@ -1,9 +1,9 @@
 
-QC Plots UMIs — QC_Plots_UMIs • scCustomizeQC Plots UMIs — QC_Plots_UMIs • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots UMIs
    
-    Source: R/QC_Plotting_Seurat.R
+    Source: R/Plotting_QC_Seurat.R
     
     
    
 
@@ -124,6 +130,7 @@ 
    QC Plots UMIs
    
   y_axis_label = "UMIs",
   low_cutoff = NULL,
   high_cutoff = NULL,
+  cutoff_line_width = NULL,
   pt.size = NULL,
   plot_median = FALSE,
   median_size = 15,
@@ -140,87 +147,91 @@ 
    QC Plots UMIs
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    plot_title
    
+
    plot_title
    
 
    Plot Title.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.
    
 
 
-
    x_axis_label
    
+
    x_axis_label
    
 
    Label for x axis.
    
 
 
-
    y_axis_label
    
+
    y_axis_label
    
 
    Label for y axis.
    
 
 
-
    low_cutoff
    
+
    low_cutoff
    
 
    Plot line a potential low threshold for filtering.
    
 
 
-
    high_cutoff
    
+
    high_cutoff
    
 
    Plot line a potential high threshold for filtering.
    
 
 
-
    pt.size
    
+
    cutoff_line_width
    
+
    numerical value for thickness of cutoff lines, default is NULL.
    
+
+
+
    pt.size
    
 
    Point size for plotting.
    
 
 
-
    plot_median
    
+
    plot_median
    
 
    logical, whether to plot median for each ident on the plot (Default is FALSE).
    
 
 
-
    median_size
    
+
    median_size
    
 
    Shape size for the median is plotted.
    
 
 
-
    plot_boxplot
    
+
    plot_boxplot
    
 
    logical, whether to plot boxplot inside of violin (Default is FALSE).
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    vector of colors to use for plot.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    Rotate x-axis labels 45 degrees (Default is TRUE).
    
 
 
-
    y_axis_log
    
+
    y_axis_log
    
 
    logical. Whether to change y axis to log10 scale (Default is FALSE).
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to VlnPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -244,15 +255,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Random_Cells_Downsample.html b/docs/reference/Random_Cells_Downsample.html
new file mode 100644
index 0000000000..98bebd287a
--- /dev/null
+++ b/docs/reference/Random_Cells_Downsample.html
@@ -0,0 +1,237 @@
+
+Randomly downsample by identity — Random_Cells_Downsample • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Randomly downsample by identity
    
+    Source: R/Object_Utilities.R
+    
+    
    
+
+    
    
+    
    Get a randomly downsampled set of cell barcodes with even numbers of cells for each identity class.
+Can return either as a list (1 entry per identity class) or vector of barcodes.
    
+    
    
+
+    
    
+    
    Random_Cells_Downsample(
+  seurat_object,
+  num_cells,
+  group.by = "ident",
+  return_list = FALSE,
+  allow_lower = FALSE,
+  seed = 123
+)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    seurat_object
    
+
    Seurat object
    
+
+
+
    num_cells
    
+
    number of cells per ident to use in down-sampling.  This value must be less than or
+equal to the size of ident with fewest cells.  Alternatively, can set to "min" which will
+use the maximum number of barcodes based on size of smallest group.
    
+
+
+
    group.by
    
+
    The ident to use to group cells.  Default is "ident" which use current active.ident.  .
    
+
+
+
    return_list
    
+
    logical, whether or not to return the results as list instead of vector, default is
+FALSE.
    
+
+
+
    allow_lower
    
+
    logical, if number of cells in identity is lower than num_cells keep the
+maximum number of cells, default is FALSE.  If FALSE will report error message if num_cells is
+too high, if TRUE will subset cells with more than num_cells to that value and those with less
+than num_cells will not be downsampled.
    
+
+
+
    seed
    
+
    random seed to use for downsampling.  Default is 123.
    
+
+
    
+    
    
+    
    Value
    
+    
    either a vector or list of cell barcodes
    
+    
    
+
+    
    
+    
    Examples
    
+    
    library(Seurat)
+
+# return vector of barcodes
+random_cells <- Random_Cells_Downsample(seurat_object = pbmc_small, num_cells = 10)
+head(random_cells)
+#> [1] "GTCATACTTCGCCT" "GCGCATCTTGCTCC" "TACTCTGAATCGAC" "GAACCTGATGAACC"
+#> [5] "AATGTTGACAGTCA" "GGCATATGCTTATC"
+
+# return list
+random_cells_list <- Random_Cells_Downsample(seurat_object = pbmc_small, return_list = TRUE,
+num_cells = 10)
+head(random_cells_list)
+#> [[1]]
+#>  [1] "GTCATACTTCGCCT" "GCGCATCTTGCTCC" "TACTCTGAATCGAC" "GAACCTGATGAACC"
+#>  [5] "AATGTTGACAGTCA" "GGCATATGCTTATC" "CTTCATGACCGAAT" "CTAAACCTCTGACA"
+#>  [9] "AGTCAGACTGCACA" "TAGGGACTGAACTC"
+#> 
+#> [[2]]
+#>  [1] "AAGCGACTTTGACG" "ATTGTAGATTCCCG" "ATTACCTGCCTTAT" "ATACCACTCTAAGC"
+#>  [5] "TCCACTCTGAGCTT" "GCGCACGACTTTAC" "CCATCCGATTCGCC" "AAATTCGAATCACG"
+#>  [9] "CATCAGGATGCACA" "ACGTGATGCCATGA"
+#> 
+#> [[3]]
+#>  [1] "GCGTAAACACGGTT" "CATGAGACACGGGA" "TTGCATTGAGCTAC" "AGGTCATGAGTGTC"
+#>  [5] "GATAGAGAAGGGTG" "GTAAGCACTCATTC" "TACGCCACTCCGAA" "GCTCCATGAGAAGT"
+#>  [9] "TACATCACGCTAAC" "CATATAGACTAAGC"
+#> 
+
+# return max total number of cells (setting `num_cells = "min`)
+random_cells_max <- Random_Cells_Downsample(seurat_object = pbmc_small, num_cells = "min")
+#> The number of cells was set to "min", returning 19 cells per identity class
+#> (equal to size of smallest identity class(es): "2").
+#> ✔ Total of 57 cells across whole object.
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Read10X_GEO.html b/docs/reference/Read10X_GEO.html
index 15071889b2..a7ed19c3c2 100644
--- a/docs/reference/Read10X_GEO.html
+++ b/docs/reference/Read10X_GEO.html
@@ -1,10 +1,10 @@
 
-Load in NCBI GEO data from 10X — Read10X_GEO • scCustomizeLoad in NCBI GEO data from 10X — Read10X_GEO • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -134,47 +140,49 @@ 
    Load in NCBI GEO data from 10X
    
 
     
    
     
    Arguments
    
-    
    data_dir
    
+
+
+
    data_dir
    
 
    Directory containing the matrix.mtx, genes.tsv (or features.tsv), and barcodes.tsv
 files provided by 10X.
    
 
 
-
    sample_list
    
+
    sample_list
    
 
    A vector of file prefixes/names if specific samples are desired.  Default is NULL and
 will load all samples in given directory.
    
 
 
-
    sample_names
    
+
    sample_names
    
 
    a set of sample names to use for each sample entry in returned list.  If NULL will
 set names to the file name of each sample.
    
 
 
-
    gene.column
    
+
    gene.column
    
 
    Specify which column of genes.tsv or features.tsv to use for gene names; default is 2.
    
 
 
-
    cell.column
    
+
    cell.column
    
 
    Specify which column of barcodes.tsv to use for cell names; default is 1.
    
 
 
-
    unique.features
    
+
    unique.features
    
 
    Make feature names unique (default TRUE).
    
 
 
-
    strip.suffix
    
+
    strip.suffix
    
 
    Remove trailing "-1" if present in all cell barcodes.
    
 
 
-
    parallel
    
+
    parallel
    
 
    logical (default FALSE).  Whether to use multiple cores when reading in data.
 Only possible on Linux based systems.
    
 
 
-
    num_cores
    
+
    num_cores
    
 
    if parallel = TRUE indicates the number of cores to use for multicore processing.
    
 
 
-
    merge
    
+
    merge
    
 
    logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.
    
@@ -182,9 +190,7 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    If features.csv indicates the data has multiple data types, a list
+    
    If features.csv indicates the data has multiple data types, a list
 containing a sparse matrix of the data from each type will be returned.
 Otherwise a sparse matrix containing the expression data will be returned.
    
     
    
@@ -198,12 +204,12 @@ 
    References
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data_dir <- 'path/to/data/directory'
 expression_matrices <- Read10X_GEO(data_dir = data_dir)
 # To create object from single file
-seurat_object = CreateSeuratObject(counts = expression_matrices[[1]])
-}
+seurat_object = CreateSeuratObject(counts = expression_matrices[[1]])
+} # }
 
 
    
     
    
@@ -219,15 +225,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Read10X_Multi_Directory.html b/docs/reference/Read10X_Multi_Directory.html
index 4db57a125b..5848eaa1f8 100644
--- a/docs/reference/Read10X_Multi_Directory.html
+++ b/docs/reference/Read10X_Multi_Directory.html
@@ -1,11 +1,11 @@
 
-Load 10X count matrices from multiple directories — Read10X_Multi_Directory • scCustomizeLoad 10X count matrices from multiple directories — Read10X_Multi_Directory • scCustomize
-    
+
 
     
    
       
    
 
@@ -33,7 +33,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -136,64 +142,64 @@ 
    Load 10X count matrices from multiple directories
    
 
     
    
     
    Arguments
    
-    
    base_path
    
+
+
+
    base_path
    
 
    path to the parent directory which contains all of the subdirectories of interest.
    
 
 
-
    secondary_path
    
+
    secondary_path
    
 
    path from the parent directory to count matrix files for each sample.
    
 
 
-
    default_10X_path
    
+
    default_10X_path
    
 
    logical (default TRUE) sets the secondary path variable to the default 10X
 directory structure.
    
 
 
-
    cellranger_multi
    
+
    cellranger_multi
    
 
    logical, whether samples were processed with Cell Ranger multi, default is FALSE.
    
 
 
-
    sample_list
    
+
    sample_list
    
 
    a vector of sample directory names if only specific samples are desired.  If NULL will
 read in subdirectories in parent directory.
    
 
 
-
    sample_names
    
+
    sample_names
    
 
    a set of sample names to use for each sample entry in returned list.  If NULL will
 set names to the subdirectory name of each sample.
    
 
 
-
    parallel
    
+
    parallel
    
 
    logical (default FALSE) whether or not to use multi core processing to read in matrices.
    
 
 
-
    num_cores
    
+
    num_cores
    
 
    how many cores to use for parallel processing.
    
 
 
-
    merge
    
+
    merge
    
 
    logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to Read10X.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    a list of sparse matrices (merge = FALSE) or a single sparse matrix (merge = TRUE).
    
+    
    a list of sparse matrices (merge = FALSE) or a single sparse matrix (merge = TRUE).
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 base_path <- 'path/to/data/directory'
 expression_matrices <- Read10X_Multi_Directory(base_path = base_path)
-}
+} # }
 
 
    
     
    
@@ -209,15 +215,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Read10X_h5_GEO.html b/docs/reference/Read10X_h5_GEO.html
index 4d027ffee7..6e0b824df2 100644
--- a/docs/reference/Read10X_h5_GEO.html
+++ b/docs/reference/Read10X_h5_GEO.html
@@ -1,10 +1,10 @@
 
-Load in NCBI GEO data from 10X in HDF5 file format — Read10X_h5_GEO • scCustomizeLoad in NCBI GEO data from 10X in HDF5 file format — Read10X_h5_GEO • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -132,60 +138,60 @@ 
    Load in NCBI GEO data from 10X in HDF5 file format
    
 
     
    
     
    Arguments
    
-    
    data_dir
    
+
+
+
    data_dir
    
 
    Directory containing the .h5 files provided by 10X.
    
 
 
-
    sample_list
    
+
    sample_list
    
 
    A vector of file prefixes/names if specific samples are desired.  Default is NULL and
 will load all samples in given directory.
    
 
 
-
    sample_names
    
+
    sample_names
    
 
    a set of sample names to use for each sample entry in returned list.  If NULL
 will set names to the file name of each sample.
    
 
 
-
    shared_suffix
    
+
    shared_suffix
    
 
    a suffix and file extension shared by all samples.
    
 
 
-
    parallel
    
+
    parallel
    
 
    logical (default FALSE).  Whether to use multiple cores when reading in data.
 Only possible on Linux based systems.
    
 
 
-
    num_cores
    
+
    num_cores
    
 
    if parallel = TRUE indicates the number of cores to use for multicore processing.
    
 
 
-
    merge
    
+
    merge
    
 
    logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.
    
 
 
-
    ...
    
+
    ...
    
 
    Additional arguments passed to Read10X_h5
    
 
 
    
     
    
     
    Value
    
-    
-
-
    If the data has multiple data types, a list
+    
    If the data has multiple data types, a list
 containing a sparse matrix of the data from each type will be returned.
 Otherwise a sparse matrix containing the expression data will be returned.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data_dir <- 'path/to/data/directory'
 expression_matrices <- Read10X_h5_GEO(data_dir = data_dir)
 # To create object from single file
-seurat_object = CreateSeuratObject(counts = expression_matrices[[1]])
-}
+seurat_object = CreateSeuratObject(counts = expression_matrices[[1]])
+} # }
 
 
    
     
    
@@ -201,15 +207,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Read10X_h5_Multi_Directory.html b/docs/reference/Read10X_h5_Multi_Directory.html
index 8ef690c392..43f5a1b080 100644
--- a/docs/reference/Read10X_h5_Multi_Directory.html
+++ b/docs/reference/Read10X_h5_Multi_Directory.html
@@ -1,11 +1,11 @@
 
-Load 10X h5 count matrices from multiple directories — Read10X_h5_Multi_Directory • scCustomizeLoad 10X h5 count matrices from multiple directories — Read10X_h5_Multi_Directory • scCustomize
-    
+
 
     
    
       
    
 
@@ -33,7 +33,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -126,7 +132,6 @@ 
    Load 10X h5 count matrices from multiple directories
    
   default_10X_path = TRUE,
   cellranger_multi = FALSE,
   h5_filename = "filtered_feature_bc_matrix.h5",
-  cell_bender = deprecated(),
   sample_list = NULL,
   sample_names = NULL,
   replace_suffix = FALSE,
@@ -140,86 +145,81 @@ 
    Load 10X h5 count matrices from multiple directories
    
 
     
    
     
    Arguments
    
-    
    base_path
    
+
+
+
    base_path
    
 
    path to the parent directory which contains all of the subdirectories of interest.
    
 
 
-
    secondary_path
    
+
    secondary_path
    
 
    path from the parent directory to count matrix files for each sample.
    
 
 
-
    default_10X_path
    
+
    default_10X_path
    
 
    logical (default TRUE) sets the secondary path variable to the default 10X
 directory structure.
    
 
 
-
    cellranger_multi
    
+
    cellranger_multi
    
 
    logical, whether samples were processed with Cell Ranger multi, default is FALSE.
    
 
 
-
    h5_filename
    
+
    h5_filename
    
 
    name of h5 file (including .h5 suffix).  If all h5 files have same name (i.e. Cell Ranger output)
 then use full file name.  By default function uses Cell Ranger name: "filtered_feature_bc_matrix.h5".
 If h5 files have sample specific prefixes (i.e. from Cell Bender) then use only the shared part of file
 name (e.g., "_filtered_out.h5").
    
 
 
-
    cell_bender
    
-
    [Deprecated] CellBender read functions are now independent family of functions.
-See Read_CellBender_* functions.
    
-
-
-
    sample_list
    
+
    sample_list
    
 
    a vector of sample directory names if only specific samples are desired.  If NULL will
 read in subdirectories in parent directory.
    
 
 
-
    sample_names
    
+
    sample_names
    
 
    a set of sample names to use for each sample entry in returned list.  If NULL will
 set names to the subdirectory name of each sample.
    
 
 
-
    replace_suffix
    
+
    replace_suffix
    
 
    logical (default FALSE).  Whether or not to replace the barcode suffixes of matrices
 using Replace_Suffix.
    
 
 
-
    new_suffix_list
    
+
    new_suffix_list
    
 
    a vector of new suffixes to replace existing suffixes if replace_suffix = TRUE.
 See Replace_Suffix for more information.  To remove all suffixes set new_suffix_list = "".
    
 
 
-
    parallel
    
+
    parallel
    
 
    logical (default FALSE) whether or not to use multi core processing to read in matrices.
    
 
 
-
    num_cores
    
+
    num_cores
    
 
    how many cores to use for parallel processing.
    
 
 
-
    merge
    
+
    merge
    
 
    logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to Read10X_h5.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    a list of sparse matrices (merge = FALSE) or a single sparse matrix (merge = TRUE).
    
+    
    a list of sparse matrices (merge = FALSE) or a single sparse matrix (merge = TRUE).
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 base_path <- 'path/to/data/directory'
 expression_matrices <- Read10X_h5_Multi_Directory(base_path = base_path)
-}
+} # }
 
 
    
     
    
@@ -235,15 +235,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Read_CellBender_h5_Mat.html b/docs/reference/Read_CellBender_h5_Mat.html
index 8fe0710fa2..b47dd3d6f3 100644
--- a/docs/reference/Read_CellBender_h5_Mat.html
+++ b/docs/reference/Read_CellBender_h5_Mat.html
@@ -1,9 +1,9 @@
 
-Load CellBender h5 matrices (corrected) — Read_CellBender_h5_Mat • scCustomizeLoad CellBender h5 matrices (corrected) — Read_CellBender_h5_Mat • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -127,33 +133,33 @@ 
    Load CellBender h5 matrices (corrected)
    
 
     
    
     
    Arguments
    
-    
    file_name
    
+
+
+
    file_name
    
 
    Path to h5 file.
    
 
 
-
    use.names
    
+
    use.names
    
 
    Label row names with feature names rather than ID numbers (default TRUE).
    
 
 
-
    unique.features
    
+
    unique.features
    
 
    Make feature names unique (default TRUE).
    
 
 
-
    h5_group_name
    
+
    h5_group_name
    
 
    Name of the group within H5 file that contains count data.  This is only
 required if H5 file contains multiple subgroups and non-default names.  Default is NULL.
    
 
 
-
    feature_slot_name
    
+
    feature_slot_name
    
 
    Name of the slot contain feature names/ids.  Must be one of:
 "features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo).  Default is "features".
    
 
 
    
     
    
     
    Value
    
-    
-
-
    sparse matrix
    
+    
    sparse matrix
    
     
    
     
    
     
    References
    
@@ -163,9 +169,9 @@ 
    References
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 mat <- Read_CellBender_h5_Mat(file_name = "/SampleA_out_filtered.h5")
-}
+} # }
 
 
    
     
    
@@ -181,15 +187,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Read_CellBender_h5_Multi_Directory.html b/docs/reference/Read_CellBender_h5_Multi_Directory.html
index da319f2460..d5dd94fc3a 100644
--- a/docs/reference/Read_CellBender_h5_Multi_Directory.html
+++ b/docs/reference/Read_CellBender_h5_Multi_Directory.html
@@ -1,10 +1,10 @@
 
-Load CellBender h5 matrices (corrected) from multiple directories — Read_CellBender_h5_Multi_Directory • scCustomizeLoad CellBender h5 matrices (corrected) from multiple directories — Read_CellBender_h5_Multi_Directory • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -138,84 +144,85 @@ 
    Load CellBender h5 matrices (corrected) from multiple directories
    
 
     
    
     
    Arguments
    
-    
    base_path
    
+
+
+
    base_path
    
 
    path to the parent directory which contains all of the subdirectories of interest.
    
 
 
-
    secondary_path
    
+
    secondary_path
    
 
    path from the parent directory to count matrix files for each sample.
    
 
 
-
    filtered_h5
    
+
    filtered_h5
    
 
    logical (default TRUE).  Will set the shared file name suffix custom_name is NULL.
    
 
 
-
    custom_name
    
+
    custom_name
    
 
    if file name was customized in CellBender then this parameter should contain the portion
 of file name that is shared across all samples.  Must included the ".h5" extension as well.
    
 
 
-
    sample_list
    
+
    sample_list
    
 
    a vector of sample directory names if only specific samples are desired.  If NULL will
 read in subdirectories in parent directory.
    
 
 
-
    sample_names
    
+
    sample_names
    
 
    a set of sample names to use for each sample entry in returned list.  If NULL will
-set names to the subdirectory name of each sample.
    
+set names to the subdirectory name of each sample.  NOTE: unless sample_list is specified this will
+rename files in the order they are read which will be alphabetical.
    
 
 
-
    h5_group_name
    
+
    h5_group_name
    
 
    Name of the group within H5 file that contains count data.  This is only
 required if H5 file contains multiple subgroups and non-default names.  Default is NULL.
    
 
 
-
    feature_slot_name
    
+
    feature_slot_name
    
 
    Name of the slot contain feature names/ids.  Must be one of:
 "features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo).  Default is "features".
    
 
 
-
    replace_suffix
    
+
    replace_suffix
    
 
    logical (default FALSE).  Whether or not to replace the barcode suffixes of matrices
 using Replace_Suffix.
    
 
 
-
    new_suffix_list
    
+
    new_suffix_list
    
 
    a vector of new suffixes to replace existing suffixes if replace_suffix = TRUE.
 See Replace_Suffix for more information.  To remove all suffixes set new_suffix_list = "".
    
 
 
-
    parallel
    
+
    parallel
    
 
    logical (default FALSE) whether or not to use multi core processing to read in matrices.
    
 
 
-
    num_cores
    
+
    num_cores
    
 
    how many cores to use for parallel processing.
    
 
 
-
    merge
    
+
    merge
    
 
    logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to Read_CellBender_h5_Mat.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    list of sparse matrices
    
+    
    list of sparse matrices
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 base_path <- 'path/to/data/directory'
 mat_list <- Read_CellBender_h5_Multi_Directory(base_path = base_path)
-}
+} # }
 
 
    
     
    
@@ -231,15 +238,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Read_CellBender_h5_Multi_File.html b/docs/reference/Read_CellBender_h5_Multi_File.html
index 221de9a083..6fa4ec2e7d 100644
--- a/docs/reference/Read_CellBender_h5_Multi_File.html
+++ b/docs/reference/Read_CellBender_h5_Multi_File.html
@@ -1,10 +1,10 @@
 
-Load CellBender h5 matrices (corrected) from multiple files — Read_CellBender_h5_Multi_File • scCustomizeLoad CellBender h5 matrices (corrected) from multiple files — Read_CellBender_h5_Multi_File • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -135,70 +141,70 @@ 
    Load CellBender h5 matrices (corrected) from multiple files
    
 
     
    
     
    Arguments
    
-    
    data_dir
    
+
+
+
    data_dir
    
 
    Directory containing the .h5 files output by CellBender.
    
 
 
-
    filtered_h5
    
+
    filtered_h5
    
 
    logical (default TRUE).  Will set the shared file name suffix if custom_name is NULL.
    
 
 
-
    custom_name
    
+
    custom_name
    
 
    if file name was customized in CellBender then this parameter should contain the portion
 of file name that is shared across all samples.  Must included the ".h5" extension as well.
    
 
 
-
    sample_list
    
+
    sample_list
    
 
    a vector of sample names if only specific samples are desired.  If NULL will
 read in all files within data_dir directory.
    
 
 
-
    sample_names
    
+
    sample_names
    
 
    a set of sample names to use for each sample entry in returned list.  If NULL will
 set names to the subdirectory name of each sample.
    
 
 
-
    h5_group_name
    
+
    h5_group_name
    
 
    Name of the group within H5 file that contains count data.  This is only
 required if H5 file contains multiple subgroups and non-default names.  Default is NULL.
    
 
 
-
    feature_slot_name
    
+
    feature_slot_name
    
 
    Name of the slot contain feature names/ids.  Must be one of:
 "features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo).  Default is "features".
    
 
 
-
    parallel
    
+
    parallel
    
 
    logical (default FALSE) whether or not to use multi core processing to read in matrices
    
 
 
-
    num_cores
    
+
    num_cores
    
 
    how many cores to use for parallel processing.
    
 
 
-
    merge
    
+
    merge
    
 
    logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to Read_CellBender_h5_Mat.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    list of sparse matrices
    
+    
    list of sparse matrices
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 base_path <- 'path/to/data/directory'
 mat_list <- Read_CellBender_h5_Multi_File(data_dir = base_path)
-}
+} # }
 
 
    
     
    
@@ -214,15 +220,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Read_GEO_Delim.html b/docs/reference/Read_GEO_Delim.html
index 189aee1c99..17d94a2355 100644
--- a/docs/reference/Read_GEO_Delim.html
+++ b/docs/reference/Read_GEO_Delim.html
@@ -1,9 +1,9 @@
 
-Load in NCBI GEO data formatted as single file per sample — Read_GEO_Delim • scCustomizeLoad in NCBI GEO data formatted as single file per sample — Read_GEO_Delim • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -132,52 +138,54 @@ 
    Load in NCBI GEO data formatted as single file per sample
    
 
     
    
     
    Arguments
    
-    
    data_dir
    
+
+
+
    data_dir
    
 
    Directory containing the files.
    
 
 
-
    file_suffix
    
+
    file_suffix
    
 
    The file suffix of the individual files.  Must be the same across all files being
 imported.  This is used to detect files to import and their GEO IDs.
    
 
 
-
    move_genes_rownames
    
+
    move_genes_rownames
    
 
    logical.  Whether gene IDs are present in first column or in row names of
 delimited file.  If TRUE will move the first column to row names before creating final matrix.
 Default is TRUE.
    
 
 
-
    sample_list
    
+
    sample_list
    
 
    a vector of samples within directory to read in (can be either with or
 without file_suffix see full_names).  If NULL will read in all subdirectories.
    
 
 
-
    full_names
    
+
    full_names
    
 
    logical (default FALSE).  Whether or not the sample_list vector includes the file suffix.
 If FALSE the function will add suffix based on file_suffix parameter.
    
 
 
-
    sample_names
    
+
    sample_names
    
 
    a set of sample names to use for each sample entry in returned list.
 If NULL will set names to the directory name of each sample.
    
 
 
-
    barcode_suffix_period
    
+
    barcode_suffix_period
    
 
    Is the barcode suffix a period and should it be changed to "-".  Default (FALSE;
 barcodes will be left identical to their format in input files.).  If TRUE "." in barcode suffix will
 be changed to "-".
    
 
 
-
    parallel
    
+
    parallel
    
 
    logical (default FALSE).  Whether to use multiple cores when reading in data.
 Only possible on Linux based systems.
    
 
 
-
    num_cores
    
+
    num_cores
    
 
    if parallel = TRUE indicates the number of cores to use for multicore processing.
    
 
 
-
    merge
    
+
    merge
    
 
    logical (default FALSE) whether or not to merge samples into a single matrix or return
 list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
 will be taken from sample_names.
    
@@ -185,17 +193,15 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    List of gene x cell matrices in list format named by sample name.
    
+    
    List of gene x cell matrices in list format named by sample name.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data_dir <- 'path/to/data/directory'
 expression_matrices <- Read_GEO_Delim(data_dir = data_dir)
-}
+} # }
 
 
    
     
    
@@ -211,15 +217,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Read_Metrics_10X.html b/docs/reference/Read_Metrics_10X.html
index a0f6791646..55b7bff9bb 100644
--- a/docs/reference/Read_Metrics_10X.html
+++ b/docs/reference/Read_Metrics_10X.html
@@ -1,9 +1,9 @@
 
-Read Overall Statistics from 10X Cell Ranger Count — Read_Metrics_10X • scCustomizeRead Overall Statistics from 10X Cell Ranger Count — Read_Metrics_10X • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -128,45 +134,46 @@ 
    Read Overall Statistics from 10X Cell Ranger Count
    
 
     
    
     
    Arguments
    
-    
    base_path
    
-
    path to the parent directory which contains all of the subdirectories of interest.
    
 
 
-
    secondary_path
    
+
    base_path
    
+
    path to the parent directory which contains all of the subdirectories of interest or
+alternatively can provide single csv file to read and format identically to reading multiple files.
    
+
+
+
    secondary_path
    
 
    path from the parent directory to count "outs/" folder which contains the
 "metrics_summary.csv" file.
    
 
 
-
    default_10X
    
+
    default_10X
    
 
    logical (default TRUE) sets the secondary path variable to the default 10X directory structure.
    
 
 
-
    cellranger_multi
    
+
    cellranger_multi
    
 
    logical, whether or not metrics come from Cell Ranger count or from Cell Ranger multi.  Default is FALSE.
    
 
 
-
    lib_list
    
+
    lib_list
    
 
    a list of sample names (matching directory names) to import.  If NULL will read
 in all samples in parent directory.
    
 
 
-
    lib_names
    
+
    lib_names
    
 
    a set of sample names to use for each sample.  If NULL will set names to the
 directory name of each sample.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A data frame with sample metrics from cell ranger.
    
+    
    A data frame or list of data.frames with sample metrics from cell ranger.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 metrics <- Read_Metrics_10X(base_path = "/path/to/directories", default_10X = TRUE)
-}
+} # }
 
 
    
     
    
@@ -182,15 +189,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Read_Metrics_CellBender.html b/docs/reference/Read_Metrics_CellBender.html
new file mode 100644
index 0000000000..74d1e50f3c
--- /dev/null
+++ b/docs/reference/Read_Metrics_CellBender.html
@@ -0,0 +1,183 @@
+
+Read Overall Statistics from CellBender — Read_Metrics_CellBender • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Read Overall Statistics from CellBender
    
+    Source: R/Read_&_Write_Data.R
+    
+    
    
+
+    
    
+    
    Get data.frame with all metrics from the CellBender remove-background analysis.
    
+    
    
+
+    
    
+    
    Read_Metrics_CellBender(base_path, lib_list = NULL, lib_names = NULL)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    base_path
    
+
    path to the parent directory which contains all of the sub-directories of interest or
+path to single metrics csv file.
    
+
+
+
    lib_list
    
+
    a list of sample names (matching directory names) to import.  If NULL will read
+in all samples in parent directory.
    
+
+
+
    lib_names
    
+
    a set of sample names to use for each sample.  If NULL will set names to the
+directory name of each sample.
    
+
+
    
+    
    
+    
    Value
    
+    
    A data frame with sample metrics from CellBender.
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+CB_metrics <- Read_Metrics_CellBender(base_path = "/path/to/directories")
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Reduction_Loading_Present.html b/docs/reference/Reduction_Loading_Present.html
index 95672cc9b5..8521bc5b0d 100644
--- a/docs/reference/Reduction_Loading_Present.html
+++ b/docs/reference/Reduction_Loading_Present.html
@@ -1,10 +1,10 @@
 
-Check if reduction loadings are present — Reduction_Loading_Present • scCustomizeCheck if reduction loadings are present — Reduction_Loading_Present • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -129,41 +135,41 @@ 
    Check if reduction loadings are present
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    object name.
    
 
 
-
    reduction_names
    
+
    reduction_names
    
 
    vector of genes to check.
    
 
 
-
    print_msg
    
+
    print_msg
    
 
    logical. Whether message should be printed if all features are found.  Default is TRUE.
    
 
 
-
    omit_warn
    
+
    omit_warn
    
 
    logical. Whether to print message about features that are not found in current object.
 Default is TRUE.
    
 
 
-
    return_none
    
+
    return_none
    
 
    logical. Whether list of found vs. bad features should still be returned if no
 features are found.  Default is FALSE.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A list of length 3 containing 1) found features, 2) not found features.
    
+    
    A list of length 3 containing 1) found features, 2) not found features.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 reductions <- Reduction_Loading_Present(seurat_object = obj_name, reduction_name = "PC_1")
-found_features <- features[[1]]
-}
+found_reductions <- reductions[[1]]
+} # }
 
 
    
     
    
@@ -179,15 +185,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Rename_Clusters.Seurat.html b/docs/reference/Rename_Clusters.Seurat.html
new file mode 100644
index 0000000000..89fb94f7d8
--- /dev/null
+++ b/docs/reference/Rename_Clusters.Seurat.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Rename_Clusters.html b/docs/reference/Rename_Clusters.html
index b8ebcc94f0..bdc582ad90 100644
--- a/docs/reference/Rename_Clusters.html
+++ b/docs/reference/Rename_Clusters.html
@@ -1,9 +1,9 @@
 
-Rename Cluster Seurat — Rename_Clusters • scCustomizeRename Clusters — Rename_Clusters • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
-    
    Rename Cluster Seurat
    
-    Source: R/Utilities.R
+    
    Rename Clusters
    
+    Source: R/Generics.R, R/LIGER_Utilities.R, R/Utilities.R
     
     
    
 
     
    
-    
    Wrapper function to rename active identities in Seurat Object with new idents.
    
+    
    Wrapper function to rename active cluster identity in Seurat or Liger Object with new idents.
    
     
    
 
     
    
-    
    Rename_Clusters(seurat_object, new_idents, meta_col_name = NULL, ...)
    
+    
    Rename_Clusters(object, ...)
+
+# S3 method for class 'liger'
+Rename_Clusters(
+  object,
+  new_idents,
+  old_ident_name = NULL,
+  new_ident_name = NULL,
+  overwrite = FALSE,
+  ...
+)
+
+# S3 method for class 'Seurat'
+Rename_Clusters(
+  object,
+  new_idents,
+  old_ident_name = NULL,
+  new_ident_name = NULL,
+  meta_col_name = deprecated(),
+  overwrite = FALSE,
+  ...
+)
    
     
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
-
    object name.
    
 
 
-
    new_idents
    
-
    vector of new cluster names.  Must be equal to the length of current active.ident
-in Seurat Object.  Will accept named vector (with old idents as names) or will name the new_idents vector internally.
    
+
    object
    
+
    Object of class Seurat or liger.
    
+
+
+
    ...
    
+
    Arguments passed to other methods
    
 
 
-
    meta_col_name
    
-
    (Optional).  Whether or not to create new named column in Object@meta.data
-to store the old identities.
    
+
    new_idents
    
+
    vector of new cluster names.  Must be equal to the length of current default identity
+of Object.  Will accept named vector (with old idents as names) or will name the new_idents vector internally.
    
 
 
-
    ...
    
-
    Extra parameters passed to RenameIdents.
    
+
    old_ident_name
    
+
    optional, name to use for storing current object idents in object meta data slot.
    
+
+
+
    new_ident_name
    
+
    optional, name to use for storing new object idents in object meta data slot.
    
+
+
+
    overwrite
    
+
    logical, whether to overwrite columns in object meta data slot. if they have same
+names as old_ident_name and/or new_ident_name.
    
+
+
+
    meta_col_name
    
+
    [Soft-deprecated]. See old_ident_name.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Seurat Object with new identities placed in active.ident slot.
    
+    
    An object of the same class as object with updated default identities.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
+# Liger version
+obj <- Rename_Clusters(object = obj_name, new_idents = new_idents_vec,
+old_ident_name = "LIGER_Idents_Round01", new_ident_name = "LIGER_Idents_Round02")
+} # }
+
+if (FALSE) { # \dontrun{
 obj <- Rename_Clusters(seurat_object = obj_name, new_idents = new_idents_vec,
-meta_col_name = "Round01_Res0.6_Idents")
-}
+old_ident_name = "Seurat_Idents_Round01", new_ident_name = "Round01_Res0.6_Idents")
+} # }
 
 
    
     
    
@@ -167,15 +212,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Rename_Clusters.liger.html b/docs/reference/Rename_Clusters.liger.html
new file mode 100644
index 0000000000..89fb94f7d8
--- /dev/null
+++ b/docs/reference/Rename_Clusters.liger.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/Replace_Suffix.html b/docs/reference/Replace_Suffix.html
index b7584f6410..7f454c3971 100644
--- a/docs/reference/Replace_Suffix.html
+++ b/docs/reference/Replace_Suffix.html
@@ -1,9 +1,9 @@
 
-Replace barcode suffixes — Replace_Suffix • scCustomizeReplace barcode suffixes — Replace_Suffix • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,16 +127,18 @@ 
    Replace barcode suffixes
    
 
     
    
     
    Arguments
    
-    
    data
    
+
+
+
    data
    
 
    Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.
    
 
 
-
    current_suffix
    
+
    current_suffix
    
 
    a single value or vector of values representing current barcode suffix.
 If suffix is the same for all matrices/data.frames in list only single value is required.
    
 
 
-
    new_suffix
    
+
    new_suffix
    
 
    a single value or vector of values representing new barcode suffix to be added.
 If desired suffix is the same for all matrices/data.frames in list only single value is required.
 If no suffix is desired set new_suffix = "".`
    
@@ -138,16 +146,14 @@ 
    Arguments
    
 
    
     
    
     
    Value
    
-    
-
-
    matrix or data.frame with new column names.
    
+    
    matrix or data.frame with new column names.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 dge_matrix <- Replace_Suffix(data = dge_matrix, current_suffix = "-1", new_suffix = "-2")
-}
+} # }
 
 
    
     
    
@@ -163,15 +169,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Alignment_Combined.html b/docs/reference/Seq_QC_Plot_Alignment_Combined.html
index 61a02e9bdb..c0a0c560b0 100644
--- a/docs/reference/Seq_QC_Plot_Alignment_Combined.html
+++ b/docs/reference/Seq_QC_Plot_Alignment_Combined.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics (Alignment) (Layout) — Seq_QC_Plot_Alignment_Combined • scCustomizeQC Plots Sequencing metrics (Alignment) (Layout) — Seq_QC_Plot_Alignment_Combined • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics (Alignment) (Layout)
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -130,52 +136,52 @@ 
    QC Plots Sequencing metrics (Alignment) (Layout)
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    patchwork_title
    
+
    patchwork_title
    
 
    Title to use for the patchworked plot output.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Alignment_Combined(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -191,15 +197,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Antisense.html b/docs/reference/Seq_QC_Plot_Antisense.html
index bef4ae77c4..c1f5a18649 100644
--- a/docs/reference/Seq_QC_Plot_Antisense.html
+++ b/docs/reference/Seq_QC_Plot_Antisense.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Antisense • scCustomizeQC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Antisense • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics (Alignment)
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics (Alignment)
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Antisense(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Basic_Combined.html b/docs/reference/Seq_QC_Plot_Basic_Combined.html
index fec3e091a4..51a36994b5 100644
--- a/docs/reference/Seq_QC_Plot_Basic_Combined.html
+++ b/docs/reference/Seq_QC_Plot_Basic_Combined.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics (Layout) — Seq_QC_Plot_Basic_Combined • scCustomizeQC Plots Sequencing metrics (Layout) — Seq_QC_Plot_Basic_Combined • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics (Layout)
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -130,52 +136,52 @@ 
    QC Plots Sequencing metrics (Layout)
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    patchwork_title
    
+
    patchwork_title
    
 
    Title to use for the patchworked plot output.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Basic_Combined(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -191,15 +197,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Exonic.html b/docs/reference/Seq_QC_Plot_Exonic.html
index 7de464d9e2..72973a22bf 100644
--- a/docs/reference/Seq_QC_Plot_Exonic.html
+++ b/docs/reference/Seq_QC_Plot_Exonic.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Exonic • scCustomizeQC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Exonic • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics (Alignment)
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics (Alignment)
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Exonic(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Genes.html b/docs/reference/Seq_QC_Plot_Genes.html
index 7bc2dee072..f5f7e64ed0 100644
--- a/docs/reference/Seq_QC_Plot_Genes.html
+++ b/docs/reference/Seq_QC_Plot_Genes.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics — Seq_QC_Plot_Genes • scCustomizeQC Plots Sequencing metrics — Seq_QC_Plot_Genes • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Genes(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Genome.html b/docs/reference/Seq_QC_Plot_Genome.html
index eff3019820..2c23778e8b 100644
--- a/docs/reference/Seq_QC_Plot_Genome.html
+++ b/docs/reference/Seq_QC_Plot_Genome.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Genome • scCustomizeQC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Genome • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics (Alignment)
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics (Alignment)
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Genome(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Intergenic.html b/docs/reference/Seq_QC_Plot_Intergenic.html
index ac09830969..0547dd2e47 100644
--- a/docs/reference/Seq_QC_Plot_Intergenic.html
+++ b/docs/reference/Seq_QC_Plot_Intergenic.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Intergenic • scCustomizeQC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Intergenic • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics (Alignment)
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics (Alignment)
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Intergeneic(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Intronic.html b/docs/reference/Seq_QC_Plot_Intronic.html
index 034e3f7b63..b2e021a101 100644
--- a/docs/reference/Seq_QC_Plot_Intronic.html
+++ b/docs/reference/Seq_QC_Plot_Intronic.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Intronic • scCustomizeQC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Intronic • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics (Alignment)
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics (Alignment)
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Intronic(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Number_Cells.html b/docs/reference/Seq_QC_Plot_Number_Cells.html
index f48982a150..7894a4293d 100644
--- a/docs/reference/Seq_QC_Plot_Number_Cells.html
+++ b/docs/reference/Seq_QC_Plot_Number_Cells.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics — Seq_QC_Plot_Number_Cells • scCustomizeQC Plots Sequencing metrics — Seq_QC_Plot_Number_Cells • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Number_Cells(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Reads_in_Cells.html b/docs/reference/Seq_QC_Plot_Reads_in_Cells.html
index c426232bd2..a4f7d70974 100644
--- a/docs/reference/Seq_QC_Plot_Reads_in_Cells.html
+++ b/docs/reference/Seq_QC_Plot_Reads_in_Cells.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics — Seq_QC_Plot_Reads_in_Cells • scCustomizeQC Plots Sequencing metrics — Seq_QC_Plot_Reads_in_Cells • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Reads_in_Cells(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Reads_per_Cell.html b/docs/reference/Seq_QC_Plot_Reads_per_Cell.html
index 92814104af..10fe6663f3 100644
--- a/docs/reference/Seq_QC_Plot_Reads_per_Cell.html
+++ b/docs/reference/Seq_QC_Plot_Reads_per_Cell.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics — Seq_QC_Plot_Reads_per_Cell • scCustomizeQC Plots Sequencing metrics — Seq_QC_Plot_Reads_per_Cell • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Reads_per_Cell(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Saturation.html b/docs/reference/Seq_QC_Plot_Saturation.html
index ddb727fd64..5d01eaf25b 100644
--- a/docs/reference/Seq_QC_Plot_Saturation.html
+++ b/docs/reference/Seq_QC_Plot_Saturation.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics — Seq_QC_Plot_Saturation • scCustomizeQC Plots Sequencing metrics — Seq_QC_Plot_Saturation • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Saturation(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Total_Genes.html b/docs/reference/Seq_QC_Plot_Total_Genes.html
index 43d68a1fd7..f3aebe6082 100644
--- a/docs/reference/Seq_QC_Plot_Total_Genes.html
+++ b/docs/reference/Seq_QC_Plot_Total_Genes.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics — Seq_QC_Plot_Total_Genes • scCustomizeQC Plots Sequencing metrics — Seq_QC_Plot_Total_Genes • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Total_Genes(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_Transcriptome.html b/docs/reference/Seq_QC_Plot_Transcriptome.html
index 4041ff6368..b230cabda1 100644
--- a/docs/reference/Seq_QC_Plot_Transcriptome.html
+++ b/docs/reference/Seq_QC_Plot_Transcriptome.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Transcriptome • scCustomizeQC Plots Sequencing metrics (Alignment) — Seq_QC_Plot_Transcriptome • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics (Alignment)
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics (Alignment)
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame  contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_Transcriptome(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Seq_QC_Plot_UMIs.html b/docs/reference/Seq_QC_Plot_UMIs.html
index 23e78b94c7..6043fe7f9f 100644
--- a/docs/reference/Seq_QC_Plot_UMIs.html
+++ b/docs/reference/Seq_QC_Plot_UMIs.html
@@ -1,9 +1,9 @@
 
-QC Plots Sequencing metrics — Seq_QC_Plot_UMIs • scCustomizeQC Plots Sequencing metrics — Seq_QC_Plot_UMIs • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    QC Plots Sequencing metrics
    
-    Source: R/QC_Plotting_Seq_10X.R
+    Source: R/Plotting_QC_Seq_10X.R
     
     
    
 
@@ -129,48 +135,48 @@ 
    QC Plots Sequencing metrics
    
 
     
    
     
    Arguments
    
-    
    metrics_dataframe
    
+
+
+
    metrics_dataframe
    
 
    data.frame contain Cell Ranger QC Metrics (see Read_Metrics_10X).
    
 
 
-
    plot_by
    
+
    plot_by
    
 
    Grouping factor for the plot.  Default is to plot as single group with single point per sample.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plot if plotting by group.  Defaults to RColorBrewer Dark2 palette if
 less than 8 groups and DiscretePalette_scCustomize(palette = "polychrome") if more than 8.
    
 
 
-
    dot_size
    
+
    dot_size
    
 
    size of the dots plotted if plot_by is not sample_id  Default is 1.
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical.  Whether to rotate the axes labels on the x-axis.  Default is FALSE.
    
 
 
-
    significance
    
+
    significance
    
 
    logical.  Whether to calculate and plot p-value comparisons when plotting by
 grouping factor.  Default is FALSE.
    
 
 
-
    ...
    
+
    ...
    
 
    Other variables to pass to ggpubr::stat_compare_means when doing significance testing.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 Seq_QC_Plot_UMIs(metrics_dataframe = metrics)
-}
+} # }
 
 
    
     
    
@@ -186,15 +192,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Setup_scRNAseq_Project.html b/docs/reference/Setup_scRNAseq_Project.html
index f1d845ba1e..6cac78e97e 100644
--- a/docs/reference/Setup_scRNAseq_Project.html
+++ b/docs/reference/Setup_scRNAseq_Project.html
@@ -1,9 +1,9 @@
 
-Setup project directory structure — Setup_scRNAseq_Project • scCustomizeSetup project directory structure — Setup_scRNAseq_Project • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -125,32 +131,32 @@ 
    Setup project directory structure
    
 
     
    
     
    Arguments
    
-    
    custom_dir_file
    
+
+
+
    custom_dir_file
    
 
    file to file containing desired directory structure.  Default is NULL and
 will provide generic built-in directory structure.
    
 
 
-
    cluster_annotation_path
    
+
    cluster_annotation_path
    
 
    path to place cluster annotation file using Create_Cluster_Annotation_File.
    
 
 
-
    cluster_annotation_file_name
    
+
    cluster_annotation_file_name
    
 
    name to use for annotation file if created (optional).
    
 
 
    
     
    
     
    Value
    
-    
-
-
    no return value.  Creates system folders.
    
+    
    no return value.  Creates system folders.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # If using built-in directory structure.
 Setup_scRNAseq_Project()
-}
+} # }
 
 
    
     
    
@@ -166,15 +172,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Single_Color_Palette-1.png b/docs/reference/Single_Color_Palette-1.png
index 35a08a301f..01e0a9d467 100644
Binary files a/docs/reference/Single_Color_Palette-1.png and b/docs/reference/Single_Color_Palette-1.png differ
diff --git a/docs/reference/Single_Color_Palette.html b/docs/reference/Single_Color_Palette.html
index 374d9f8b94..1825503f17 100644
--- a/docs/reference/Single_Color_Palette.html
+++ b/docs/reference/Single_Color_Palette.html
@@ -1,9 +1,9 @@
 
-Single Color Palettes for Plotting — Single_Color_Palette • scCustomizeSingle Color Palettes for Plotting — Single_Color_Palette • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,24 +127,24 @@ 
    Single Color Palettes for Plotting
    
 
     
    
     
    Arguments
    
-    
    pal_color
    
+
+
+
    pal_color
    
 
    color palette to select (Options are: 'reds', 'blues',
 'greens', 'purples', 'oranges', 'grays').
    
 
 
-
    num_colors
    
+
    num_colors
    
 
    set number of colors (max = 7).
    
 
 
-
    seed_use
    
+
    seed_use
    
 
    set seed for reproducibility (default: 123).
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A vector of colors
    
+    
    A vector of colors
    
     
    
     
    
     
    References
    
@@ -166,15 +172,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/SpatialDimPlot_scCustom.html b/docs/reference/SpatialDimPlot_scCustom.html
new file mode 100644
index 0000000000..fad41ce072
--- /dev/null
+++ b/docs/reference/SpatialDimPlot_scCustom.html
@@ -0,0 +1,286 @@
+
+SpatialDimPlot with modified default settings — SpatialDimPlot_scCustom • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    SpatialDimPlot with modified default settings
    
+    Source: R/Plotting_Seurat.R
+    
+    
    
+
+    
    
+    
    Creates SpatialDimPlot with some of the settings modified from their Seurat defaults (colors_use).
    
+    
    
+
+    
    
+    
    SpatialDimPlot_scCustom(
+  seurat_object,
+  group.by = NULL,
+  images = NULL,
+  colors_use = NULL,
+  crop = TRUE,
+  label = FALSE,
+  label.size = 7,
+  label.color = "white",
+  label.box = TRUE,
+  repel = FALSE,
+  ncol = NULL,
+  pt.size.factor = 1.6,
+  alpha = c(1, 1),
+  image.alpha = 1,
+  stroke = 0.25,
+  interactive = FALSE,
+  combine = TRUE,
+  ggplot_default_colors = FALSE,
+  color_seed = 123,
+  ...
+)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    seurat_object
    
+
    Seurat object name.
    
+
+
+
    group.by
    
+
    Name of meta.data column to group the data by
    
+
+
+
    images
    
+
    Name of the images to use in the plot(s)
    
+
+
+
    colors_use
    
+
    color palette to use for plotting.  By default if number of levels plotted is less than
+or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE
+both from DiscretePalette_scCustomize.
    
+
+
+
    crop
    
+
    Crop the plot in to focus on points plotted. Set to FALSE to show
+entire background image.
    
+
+
+
    label
    
+
    Whether to label the clusters
    
+
+
+
    label.size
    
+
    Sets the size of the labels
    
+
+
+
    label.color
    
+
    Sets the color of the label text
    
+
+
+
    label.box
    
+
    Whether to put a box around the label text (geom_text vs
+geom_label)
    
+
+
+
    repel
    
+
    Repels the labels to prevent overlap
    
+
+
+
    ncol
    
+
    Number of columns if plotting multiple plots
    
+
+
+
    pt.size.factor
    
+
    Scale the size of the spots.
    
+
+
+
    alpha
    
+
    Controls opacity of spots. Provide as a vector specifying the
+min and max for SpatialFeaturePlot. For SpatialDimPlot, provide a single
+alpha value for each plot.
    
+
+
+
    image.alpha
    
+
    Adjust the opacity of the background images. Set to 0 to
+remove.
    
+
+
+
    stroke
    
+
    Control the width of the border around the spots
    
+
+
+
    interactive
    
+
    Launch an interactive SpatialDimPlot or SpatialFeaturePlot
+session, see ISpatialDimPlot or
+ISpatialFeaturePlot for more details
    
+
+
+
    combine
    
+
    Combine plots into a single gg object; note that if TRUE;
+themeing will not work when plotting multiple features/groupings
    
+
+
+
    ggplot_default_colors
    
+
    logical.  If colors_use = NULL, Whether or not to return plot using
+default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
+
+
+
    color_seed
    
+
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
+groups plotted is greater than 36.  Default = 123.
    
+
+
+
    ...
    
+
    Extra parameters passed to DimPlot.
    
+
+
    
+    
    
+    
    Value
    
+    
    A ggplot object
    
+    
    
+    
    
+    
    References
    
+    
    Many of the param names and descriptions are from Seurat to facilitate ease of use as
+this is simply a wrapper to alter some of the default parameters https://github.com/satijalab/seurat/blob/master/R/visualization.R (License: GPL-3).
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+SpatialDimPlot_scCustom(seurat_object = seurat_object)
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Split_Layers.html b/docs/reference/Split_Layers.html
index 5cc2c10557..7b93c2e38a 100644
--- a/docs/reference/Split_Layers.html
+++ b/docs/reference/Split_Layers.html
@@ -1,9 +1,9 @@
 
-Split Seurat object into layers — Split_Layers • scCustomizeSplit Seurat object into layers — Split_Layers • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,25 +127,27 @@ 
    Split Seurat object into layers
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    assay
    
+
    assay
    
 
    name(s) of assays to convert.  Defaults to current active assay.
    
 
 
-
    split.by
    
+
    split.by
    
 
    Variable in meta.data to use for splitting layers.
    
 
 
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # Split object by "treatment"
 obj <- Split_Layers(object = obj, assay = "RNA", split.by = "treatment")
-}
+} # }
 
 
    
     
    
@@ -155,15 +163,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Split_Vector.html b/docs/reference/Split_Vector.html
index f26bd138a1..b5197b6c2c 100644
--- a/docs/reference/Split_Vector.html
+++ b/docs/reference/Split_Vector.html
@@ -1,9 +1,9 @@
 
-Split vector into list — Split_Vector • scCustomizeSplit vector into list — Split_Vector • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -116,28 +122,34 @@ 
    Split vector into list
    
     
    
 
     
    
-    
    Split_Vector(x, chunk_size = 100, verbose = FALSE)
    
+    
    Split_Vector(x, chunk_size = NULL, num_chunk = NULL, verbose = FALSE)
    
     
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    vector to split
    
 
 
-
    chunk_size
    
-
    size of chunks for vector to be split into, default is 100.
    
+
    chunk_size
    
+
    size of chunks for vector to be split into, default is NULL.  Only valid if
+num_chunk is NULL.
    
+
+
+
    num_chunk
    
+
    number of chunks to split the vector into, default is NULL.  Only valid if
+chunk_size is NULL.
    
 
 
-
    verbose
    
+
    verbose
    
 
    logical, print details of vector and split, default is FALSE.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    list with vector of X length
    
+    
    list with vector of X length
    
     
    
     
    
     
    References
    
@@ -165,15 +177,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Stacked_VlnPlot-1.png b/docs/reference/Stacked_VlnPlot-1.png
index 97527401df..82f397a23c 100644
Binary files a/docs/reference/Stacked_VlnPlot-1.png and b/docs/reference/Stacked_VlnPlot-1.png differ
diff --git a/docs/reference/Stacked_VlnPlot.html b/docs/reference/Stacked_VlnPlot.html
index 5ed98843f7..834e37d84b 100644
--- a/docs/reference/Stacked_VlnPlot.html
+++ b/docs/reference/Stacked_VlnPlot.html
@@ -1,9 +1,9 @@
 
-Stacked Violin Plot — Stacked_VlnPlot • scCustomizeStacked Violin Plot — Stacked_VlnPlot • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
     
    
     
    Stacked Violin Plot
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -139,87 +145,87 @@ 
    Stacked Violin Plot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    features
    
+
    features
    
 
    Features to plot.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Group (color) cells in different ways (for example, orig.ident).
    
 
 
-
    split.by
    
+
    split.by
    
 
    A variable to split the violin plots by,
    
 
 
-
    idents
    
+
    idents
    
 
    Which classes to include in the plot (default is all).
    
 
 
-
    x_lab_rotate
    
+
    x_lab_rotate
    
 
    logical or numeric.  If logical whether to rotate x-axis labels 45 degrees
 (Default is FALSE).  If numeric must be either 45 or 90.  Setting 45 is equivalent to setting TRUE.
    
 
 
-
    plot_legend
    
+
    plot_legend
    
 
    logical.  Adds plot legend containing idents to the returned plot.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    specify color palette to used in VlnPlot.  By default if
 number of levels plotted is less than or equal to 36 it will use "polychrome" and if greater than 36
 will use "varibow" with shuffle = TRUE both from DiscretePalette_scCustomize.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    plot_spacing
    
+
    plot_spacing
    
 
    Numerical value specifying the vertical spacing between each plot in the stack.
 Default is 0.15 ("cm").  Spacing dependent on unit provided to spacing_unit.
    
 
 
-
    spacing_unit
    
+
    spacing_unit
    
 
    Unit to use in specifying vertical spacing between plots.  Default is "cm".
    
 
 
-
    vln_linewidth
    
+
    vln_linewidth
    
 
    Adjust the linewidth of violin outline.  Must be numeric.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.  Default for Stacked_VlnPlot is 0 to avoid issues with
 rendering so many points in vector form.  Alternatively, see raster parameter.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).
    
 
 
-
    add.noise
    
+
    add.noise
    
 
    logical, determine if adding a small noise for plotting (Default is TRUE).
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to VlnPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
     
    
     
    References
    
@@ -257,15 +263,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Store_Misc_Info_Seurat.html b/docs/reference/Store_Misc_Info_Seurat.html
index 94692b3d97..bbc0749426 100644
--- a/docs/reference/Store_Misc_Info_Seurat.html
+++ b/docs/reference/Store_Misc_Info_Seurat.html
@@ -1,9 +1,9 @@
 
-Store misc data in Seurat object — Store_Misc_Info_Seurat • scCustomizeStore misc data in Seurat object — Store_Misc_Info_Seurat • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,41 +127,46 @@ 
    Store misc data in Seurat object
    
   data_to_store,
   data_name,
   list_as_list = FALSE,
-  overwrite = FALSE
+  overwrite = FALSE,
+  verbose = TRUE
 )
    
     
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    object name.
    
 
 
-
    data_to_store
    
+
    data_to_store
    
 
    data to be stored in @misc slot.  Can be single piece of data or list.
 If list of data see list_as_list parameter for control over data storage.
    
 
 
-
    data_name
    
+
    data_name
    
 
    name to give the entry in @misc slot.  Must be of equal length of the number
 of data items being stored.
    
 
 
-
    list_as_list
    
+
    list_as_list
    
 
    logical.  If data_to_store is a list, this dictates whether to store in @misc slot
 as list (TRUE) or whether to store each entry in the list separately (FALSE).  Default is FALSE.
    
 
 
-
    overwrite
    
+
    overwrite
    
 
    Logical.  Whether to overwrite existing items with the same name.  Default is FALSE, meaning
 that function will abort if item with data_name is present in misc slot.
    
 
+
+
    verbose
    
+
    logical, whether to print messages when running function, default is TRUE.
    
+
 
    
     
    
     
    Value
    
-    
-
-
    Seurat Object with new entries in the @misc slot.
    
+    
    Seurat Object with new entries in the @misc slot.
    
     
    
 
     
    
@@ -182,15 +193,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Store_Palette_Seurat.html b/docs/reference/Store_Palette_Seurat.html
index cf2c082cdd..c4261cb228 100644
--- a/docs/reference/Store_Palette_Seurat.html
+++ b/docs/reference/Store_Palette_Seurat.html
@@ -1,9 +1,9 @@
 
-Store color palette in Seurat object — Store_Palette_Seurat • scCustomizeStore color palette in Seurat object — Store_Palette_Seurat • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -121,41 +127,46 @@ 
    Store color palette in Seurat object
    
   palette,
   palette_name,
   list_as_list = FALSE,
-  overwrite = FALSE
+  overwrite = FALSE,
+  verbose = TRUE
 )
    
     
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    object name.
    
 
 
-
    palette
    
+
    palette
    
 
    vector or list of vectors containing color palettes to store.  If list of palettes
 see list_as_list parameter for control over data storage.
    
 
 
-
    palette_name
    
+
    palette_name
    
 
    name to give the palette(s) in @misc slot.  Must be of equal length to the number
 of data items being stored.
    
 
 
-
    list_as_list
    
+
    list_as_list
    
 
    logical.  If data_to_store is a list, this dictates whether to store in @misc slot
 as list (TRUE) or whether to store each entry in the list separately (FALSE).  Default is FALSE.
    
 
 
-
    overwrite
    
+
    overwrite
    
 
    Logical.  Whether to overwrite existing items with the same name.  Default is FALSE, meaning
 that function will abort if item with data_name is present in misc slot.
    
 
+
+
    verbose
    
+
    logical, whether to print messages when running function, default is TRUE.
    
+
 
    
     
    
     
    Value
    
-    
-
-
    Seurat Object with new entries in the @misc slot.
    
+    
    Seurat Object with new entries in the @misc slot.
    
     
    
 
     
    
@@ -182,15 +193,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Subset_LIGER.html b/docs/reference/Subset_LIGER.html
new file mode 100644
index 0000000000..2c2131a9f8
--- /dev/null
+++ b/docs/reference/Subset_LIGER.html
@@ -0,0 +1,211 @@
+
+Subset LIGER object — Subset_LIGER • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Subset LIGER object
    
+    Source: R/LIGER_Utilities.R
+    
+    
    
+
+    
    
+    
    Subset LIGER object by cluster or other meta data variable.
    
+    
    
+
+    
    
+    
    Subset_LIGER(
+  liger_object,
+  cluster = NULL,
+  cluster_col = "leiden_cluster",
+  ident = NULL,
+  ident_col = NULL,
+  invert = FALSE
+)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    liger_object
    
+
    LIGER object name.
    
+
+
+
    cluster
    
+
    Name(s) of cluster to subset from object.
    
+
+
+
    cluster_col
    
+
    name of @cellMeta column containing cluster names, default is "leiden_cluster".
    
+
+
+
    ident
    
+
    variable within ident_col to use in sub-setting object.
    
+
+
+
    ident_col
    
+
    column in @cellMeta that contains values provided to ident.
    
+
+
+
    invert
    
+
    logical, whether to subset the inverse of the clusters or idents provided, default is FALSE.
    
+
+
    
+    
    
+    
    Value
    
+    
    liger object
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+# subset clusters 3 and 5
+sub_liger <- subset_liger(liger_object = liger_object, cluster = c(3, 5))
+
+# subset control samples from column "Treatment"
+sub_liger <- subset_liger(liger_object = liger_object, ident = "control",
+ident_col = "Treatment")
+
+# subset control samples from column "Treatment" in clusters 3 and 5
+sub_liger <- subset_liger(liger_object = liger_object, ident = "control",
+ident_col = "Treatment", cluster = c(3, 5))
+
+# Remove cluster 9
+sub_liger <- subset_liger(liger_object = liger_object, cluster = 9, invert = TRUE)
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/Top_Genes_Factor.html b/docs/reference/Top_Genes_Factor.html
index 40162535c0..59b8333779 100644
--- a/docs/reference/Top_Genes_Factor.html
+++ b/docs/reference/Top_Genes_Factor.html
@@ -1,9 +1,9 @@
 
-Extract top loading genes for LIGER factor — Top_Genes_Factor • scCustomizeExtract top loading genes for LIGER factor — Top_Genes_Factor • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -121,30 +127,30 @@ 
    Extract top loading genes for LIGER factor
    
 
     
    
     
    Arguments
    
-    
    liger_object
    
+
+
+
    liger_object
    
 
    LIGER object name.
    
 
 
-
    liger_factor
    
+
    liger_factor
    
 
    LIGER factor number to pull genes from.
    
 
 
-
    num_genes
    
+
    num_genes
    
 
    number of top loading genes to return as vector.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A LIGER Object
    
+    
    A LIGER Object
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 top_genes_factor10 <- Top_Genes_Factor(liger_object = object, num_genes = 10)
-}
+} # }
 
 
    
     
    
@@ -160,15 +166,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/UnRotate_X-1.png b/docs/reference/UnRotate_X-1.png
index 04a5f0f45f..9eaca559c9 100644
Binary files a/docs/reference/UnRotate_X-1.png and b/docs/reference/UnRotate_X-1.png differ
diff --git a/docs/reference/UnRotate_X.html b/docs/reference/UnRotate_X.html
index a2ab19e9f3..3c569f37ae 100644
--- a/docs/reference/UnRotate_X.html
+++ b/docs/reference/UnRotate_X.html
@@ -1,9 +1,9 @@
 
-Unrotate x axis on VlnPlot — UnRotate_X • scCustomizeUnrotate x axis on VlnPlot — UnRotate_X • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -121,15 +127,15 @@ 
    Unrotate x axis on VlnPlot
    
 
     
    
     
    Arguments
    
-    
    ...
    
+
+
+
    ...
    
 
    extra arguments passed to ggplot2::theme().
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Returns a list-like object of class theme.
    
+    
    Returns a list-like object of class theme.
    
     
    
 
     
    
@@ -153,15 +159,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Updated_HGNC_Symbols.html b/docs/reference/Updated_HGNC_Symbols.html
index 14b0c61a37..2a1cf013f5 100644
--- a/docs/reference/Updated_HGNC_Symbols.html
+++ b/docs/reference/Updated_HGNC_Symbols.html
@@ -1,9 +1,9 @@
 
-Update HGNC Gene Symbols — Updated_HGNC_Symbols • scCustomizeUpdate HGNC Gene Symbols — Updated_HGNC_Symbols • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -126,7 +132,9 @@ 
    Update HGNC Gene Symbols
    
 
     
    
     
    Arguments
    
-    
    input_data
    
+
+
+
    input_data
    
 
    Data source containing gene names.  Accepted formats are:
    • charcter vector
      • 
 
    • Seurat Objects
      • 
 
    • data.frame: genes as rownames
      • 
@@ -135,36 +143,34 @@ 
      Arguments
      
 
    
 
 
-
    update_symbol_data
    
+
    update_symbol_data
    
 
    logical, whether to update cached HGNC data, default is NULL.
 If NULL BiocFileCache will check and prompt for update if cache is stale.
 If FALSE the BiocFileCache stale check will be skipped and current cache will be used.
 If TRUE the BiocFileCache stale check will be skipped and HGNC data will be downloaded.
    
 
 
-
    case_check_as_warn
    
+
    case_check_as_warn
    
 
    logical, whether case checking of features should cause abort or
 only warn, default is FALSE (abort).  Set to TRUE if atypical names (i.e. old LOC naming) are
 present in input_data.
    
 
 
-
    verbose
    
+
    verbose
    
 
    logical, whether to print results detailing numbers of symbols, found, updated,
 and not found; default is TRUE.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    data.frame containing columns: input_features, Approved_Symbol (already approved; output unchanged), Not_Found_Symbol (symbol not in HGNC; output unchanged), Updated_Symbol (new symbol from HGNC; output updated).
    
+    
    data.frame containing columns: input_features, Approved_Symbol (already approved; output unchanged), Not_Found_Symbol (symbol not in HGNC; output unchanged), Updated_Symbol (new symbol from HGNC; output updated).
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 new_names <- Updated_HGNC_Symbols(input_data = Seurat_Object)
-}
+} # }
 
 
    
     
    
@@ -180,15 +186,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Updated_MGI_Symbols.html b/docs/reference/Updated_MGI_Symbols.html
new file mode 100644
index 0000000000..16d38c03c5
--- /dev/null
+++ b/docs/reference/Updated_MGI_Symbols.html
@@ -0,0 +1,189 @@
+
+Update MGI Gene Symbols — Updated_MGI_Symbols • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Update MGI Gene Symbols
    
+    Source: R/Utilities.R
+    
+    
    
+
+    
    
+    
    Update mouse gene symbols using data from MGI  This function will store cached data in package directory using (BiocFileCache).  Use of this function requires internet connection on first use (or if setting update_symbol_data = TRUE).  Subsequent use does not require connection and will pull from cached data.
    
+    
    
+
+    
    
+    
    Updated_MGI_Symbols(input_data, update_symbol_data = NULL, verbose = TRUE)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    input_data
    
+
    Data source containing gene names.  Accepted formats are:
    • charcter vector
      • 
+
    • Seurat Objects
      • 
+
    • data.frame: genes as rownames
      • 
+
    • dgCMatrix/dgTMatrix: genes as rownames
      • 
+
    • tibble: genes in first column
      • 
+
    
+
+
+
    update_symbol_data
    
+
    logical, whether to update cached MGI data, default is NULL.
+If NULL BiocFileCache will check and prompt for update if cache is stale.
+If FALSE the BiocFileCache stale check will be skipped and current cache will be used.
+If TRUE the BiocFileCache stale check will be skipped and MGI data will be downloaded.
    
+
+
+
    verbose
    
+
    logical, whether to print results detailing numbers of symbols, found, updated,
+and not found; default is TRUE.
    
+
+
    
+    
    
+    
    Value
    
+    
    data.frame containing columns: input_features, Approved_Symbol (already approved; output unchanged), Not_Found_Symbol (symbol not in MGI; output unchanged), Updated_Symbol (new symbol from MGI; output updated).
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+new_names <- Updated_MGI_Symbols(input_data = Seurat_Object)
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/VariableFeaturePlot_scCustom-1.png b/docs/reference/VariableFeaturePlot_scCustom-1.png
index 7a696b4d76..ec6f3e4177 100644
Binary files a/docs/reference/VariableFeaturePlot_scCustom-1.png and b/docs/reference/VariableFeaturePlot_scCustom-1.png differ
diff --git a/docs/reference/VariableFeaturePlot_scCustom.html b/docs/reference/VariableFeaturePlot_scCustom.html
index 4ea01dde55..bffca73f2c 100644
--- a/docs/reference/VariableFeaturePlot_scCustom.html
+++ b/docs/reference/VariableFeaturePlot_scCustom.html
@@ -1,9 +1,9 @@
 
-Custom Labeled Variable Features Plot — VariableFeaturePlot_scCustom • scCustomizeCustom Labeled Variable Features Plot — VariableFeaturePlot_scCustom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
     
    
     
    Custom Labeled Variable Features Plot
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -133,58 +139,58 @@ 
    Custom Labeled Variable Features Plot
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    num_features
    
+
    num_features
    
 
    Number of top variable features to highlight by color/label.
    
 
 
-
    custom_features
    
+
    custom_features
    
 
    A vector of custom feature names to label on plot instead of labeling top
 variable genes.
    
 
 
-
    label
    
+
    label
    
 
    logical. Whether to label the top features.  Default is TRUE.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    colors to use for plotting.  Default is "black" and "red".
    
 
 
-
    repel
    
+
    repel
    
 
    logical (default TRUE).  Whether or not to repel the feature labels on plot.
    
 
 
-
    y_axis_log
    
+
    y_axis_log
    
 
    logical. Whether to change y axis to log10 scale (Default is FALSE).
    
 
 
-
    assay
    
+
    assay
    
 
    Assay to pull variable features from.
    
 
 
-
    selection.method
    
+
    selection.method
    
 
    If more then one method use to calculate variable features specify which
 method to use for plotting.  See selection.method parameter in VariableFeaturePlot
 for list of options.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to VariableFeaturePlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
 
     
    
@@ -208,15 +214,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/Variable_Features_ALL_LIGER.html b/docs/reference/Variable_Features_ALL_LIGER.html
index b8dcc0b178..d171921351 100644
--- a/docs/reference/Variable_Features_ALL_LIGER.html
+++ b/docs/reference/Variable_Features_ALL_LIGER.html
@@ -1,10 +1,10 @@
 
-Perform variable gene selection over whole dataset — Variable_Features_ALL_LIGER • scCustomizePerform variable gene selection over whole dataset — Variable_Features_ALL_LIGER • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -125,68 +131,69 @@ 
    Perform variable gene selection over whole dataset
    
   alpha.thresh = 0.99,
   tol = 1e-04,
   do.plot = FALSE,
-  pt.size = 0.3,
+  pt.size = 1.5,
   chunk = 1000
 )
    
     
    
 
     
    
     
    Arguments
    
-    
    liger_object
    
+
+
+
    liger_object
    
 
    LIGER object name.
    
 
 
-
    num_genes
    
+
    num_genes
    
 
    Number of genes to find. Optimizes the value of var.thresh  to get
 this number of genes, (Default is NULL).
    
 
 
-
    var.thresh
    
+
    var.thresh
    
 
    Variance threshold. Main threshold used to identify variable genes.
 Genes with expression variance greater than threshold (relative to mean) are selected.
 (higher threshold -> fewer selected genes).
    
 
 
-
    alpha.thresh
    
+
    alpha.thresh
    
 
    Alpha threshold. Controls upper bound for expected mean gene
 expression (lower threshold -> higher upper bound). (default 0.99)
    
 
 
-
    tol
    
-
    Tolerance to use for optimization if num.genes values passed in (default 0.0001).
    
+
    tol
    
+
    Tolerance to use for optimization if num.genes values passed in (default 0.0001).
+Only applicable for rliger < 2.0.0.
    
 
 
-
    do.plot
    
+
    do.plot
    
 
    Display log plot of gene variance vs. gene expression. Selected genes are
 plotted in green. (Default FALSE)
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Point size for plot.
    
 
 
-
    chunk
    
+
    chunk
    
 
    size of chunks in hdf5 file. (Default 1000)
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A LIGER Object with variable genes in correct slot.
    
+    
    A LIGER Object with variable genes in correct slot.
    
     
    
     
    
     
    References
    
-    
    Matching function parameter text descriptions are taken from rliger::selectGenes
+    
    Matching function parameter text descriptions are taken from rliger::selectGenes
 which is called by this function after creating new temporary object/dataset.
 https://github.com/welch-lab/liger. (License: GPL-3).
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 liger_obj <- Variable_Features_ALL_LIGER(liger_object = liger_obj, num_genes = 2000)
-}
+} # }
 
 
    
     
    
@@ -202,15 +209,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/VlnPlot_scCustom-1.png b/docs/reference/VlnPlot_scCustom-1.png
index 9a083c2a07..8a7aca2718 100644
Binary files a/docs/reference/VlnPlot_scCustom-1.png and b/docs/reference/VlnPlot_scCustom-1.png differ
diff --git a/docs/reference/VlnPlot_scCustom.html b/docs/reference/VlnPlot_scCustom.html
index 2ddcf07c05..ddb49acb07 100644
--- a/docs/reference/VlnPlot_scCustom.html
+++ b/docs/reference/VlnPlot_scCustom.html
@@ -1,9 +1,9 @@
 
-VlnPlot with modified default settings — VlnPlot_scCustom • scCustomizeVlnPlot with modified default settings — VlnPlot_scCustom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
     
    
     
    VlnPlot with modified default settings
    
-    Source: R/Seurat_Plotting.R
+    Source: R/Plotting_Seurat.R
     
     
    
 
@@ -138,81 +144,81 @@ 
    VlnPlot with modified default settings
    
 
     
    
     
    Arguments
    
-    
    seurat_object
    
+
+
+
    seurat_object
    
 
    Seurat object name.
    
 
 
-
    features
    
+
    features
    
 
    Feature(s) to plot.
    
 
 
-
    colors_use
    
+
    colors_use
    
 
    color palette to use for plotting.  By default if number of levels plotted is less than
 or equal to 36 it will use "polychrome" and if greater than 36 will use "varibow" with shuffle = TRUE
 both from DiscretePalette_scCustomize.
    
 
 
-
    pt.size
    
+
    pt.size
    
 
    Adjust point size for plotting.
    
 
 
-
    group.by
    
+
    group.by
    
 
    Name of one or more metadata columns to group (color) cells by (for example, orig.ident);
 default is the current active.ident of the object.
    
 
 
-
    split.by
    
+
    split.by
    
 
    Feature to split plots by (i.e. "orig.ident").
    
 
 
-
    plot_median
    
+
    plot_median
    
 
    logical, whether to plot median for each ident on the plot (Default is FALSE).
    
 
 
-
    plot_boxplot
    
+
    plot_boxplot
    
 
    logical, whether to plot boxplot inside of violin (Default is FALSE).
    
 
 
-
    median_size
    
+
    median_size
    
 
    Shape size for the median is plotted.
    
 
 
-
    idents
    
+
    idents
    
 
    Which classes to include in the plot (default is all).
    
 
 
-
    num_columns
    
+
    num_columns
    
 
    Number of columns in plot layout.  Only valid if split.by != NULL.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 100,000 total points plotted (# Cells x # of features).
    
 
 
-
    add.noise
    
+
    add.noise
    
 
    logical, determine if adding a small noise for plotting (Default is TRUE).
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "polychrome" or "varibow" palettes.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the "varibow" palette shuffle if colors_use = NULL and number of
 groups plotted is greater than 36.  Default = 123.
    
 
 
-
    ...
    
+
    ...
    
 
    Extra parameters passed to VlnPlot.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A ggplot object
    
+    
    A ggplot object
    
     
    
     
    
     
    References
    
@@ -240,15 +246,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/WhichCells.html b/docs/reference/WhichCells.html
new file mode 100644
index 0000000000..2b5f1f9a25
--- /dev/null
+++ b/docs/reference/WhichCells.html
@@ -0,0 +1,206 @@
+
+Extract Cells for particular identity — WhichCells.liger • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Extract Cells for particular identity
    
+    Source: R/LIGER_Utilities.R
+    
+    
    
+
+    
    
+    
    Extract all cell barcodes for a specific identity
    
+    
    
+
+    
    
+    
    # S3 method for class 'liger'
+WhichCells(
+  object,
+  idents = NULL,
+  ident_col = NULL,
+  by_dataset = FALSE,
+  invert = FALSE,
+  ...
+)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    object
    
+
    LIGER object name.
    
+
+
+
    idents
    
+
    identities to extract cell barcodes.
    
+
+
+
    ident_col
    
+
    name of meta data column to use when subsetting cells by identity values.
+Default is NULL, which will use the objects default clustering as the ident_col.
    
+
+
+
    by_dataset
    
+
    logical, whether to return vector with cell barcodes for all idents in or
+to return list (1 entry per dataset with vector of cells) (default is FALSE; return vector).
    
+
+
+
    invert
    
+
    logical, invert the selection of cells (default is FALSE).
    
+
+
+
    ...
    
+
    Arguments passed to other methods
    
+
+
    
+    
    
+    
    Value
    
+    
    vector or list depending on by_dataset parameter
    
+    
    
+
+    
    
+    
    Examples
    
+    
    if (FALSE) { # \dontrun{
+# Extract cells from ident =1 in current default clustering
+ident1_cells <- WhichCells(object = liger_object, idents = 1)
+
+# Extract all cells from "stim" treatment from object
+stim_cells <- WhichCells(object = liger_object, idents = "stim", ident_col = "Treatment")
+} # }
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/as.LIGER.Seurat.html b/docs/reference/as.LIGER.Seurat.html
new file mode 100644
index 0000000000..0f211365e0
--- /dev/null
+++ b/docs/reference/as.LIGER.Seurat.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/as.LIGER.html b/docs/reference/as.LIGER.html
index 75eac1d51a..c6f9c4cfb6 100644
--- a/docs/reference/as.LIGER.html
+++ b/docs/reference/as.LIGER.html
@@ -1,9 +1,9 @@
 
-Convert objects to LIGER objects — as.LIGER • scCustomizeConvert objects to LIGER objects — as.LIGER • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -118,7 +124,7 @@ 
    Convert objects to LIGER objects
    
     
    
     
    as.LIGER(x, ...)
 
-# S3 method for Seurat
+# S3 method for class 'Seurat'
 as.LIGER(
   x,
   group.by = "orig.ident",
@@ -134,7 +140,7 @@ 
    Convert objects to LIGER objects
    
   ...
 )
 
-# S3 method for list
+# S3 method for class 'list'
 as.LIGER(
   x,
   group.by = "orig.ident",
@@ -152,88 +158,86 @@ 
    Convert objects to LIGER objects
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    An object to convert to class liger
    
 
 
-
    ...
    
+
    ...
    
 
    Arguments passed to other methods
    
 
 
-
    group.by
    
+
    group.by
    
 
    Variable in meta data which contains variable to split data by, (default is "orig.ident").
    
 
 
-
    layers_name
    
+
    layers_name
    
 
    name of meta.data column used to split layers if setting group.by = "layers".
    
 
 
-
    assay
    
+
    assay
    
 
    Assay containing raw data to use, (default is "RNA").
    
 
 
-
    remove_missing
    
+
    remove_missing
    
 
    logical, whether to remove missing genes with no counts when converting to
 LIGER object (default is FALSE).
    
 
 
-
    renormalize
    
+
    renormalize
    
 
    logical, whether to perform normalization after LIGER object creation (default is TRUE).
    
 
 
-
    use_seurat_var_genes
    
+
    use_seurat_var_genes
    
 
    logical, whether to transfer variable features from Seurat object to
 new LIGER object (default is FALSE).
    
 
 
-
    use_seurat_dimreduc
    
+
    use_seurat_dimreduc
    
 
    logical, whether to transfer dimensionality reduction coordinates from
 Seurat to new LIGER object (default is FALSE).
    
 
 
-
    reduction
    
+
    reduction
    
 
    Name of Seurat reduction to transfer if use_seurat_dimreduc = TRUE.
    
 
 
-
    keep_meta
    
+
    keep_meta
    
 
    logical, whether to transfer columns in Seurat meta.data slot to LIGER cell.data
 slot (default is TRUE).
    
 
 
-
    verbose
    
+
    verbose
    
 
    logical, whether to print status messages during object conversion (default is TRUE).
    
 
 
-
    dataset_names
    
+
    dataset_names
    
 
    optional, vector of names to use for naming datasets.
    
 
 
-
    var_genes_method
    
+
    var_genes_method
    
 
    how variable genes should be selected from Seurat objects if use_seurat_var_genes = TRUE.  Can be either "intersect" or "union", (default is "intersect").
    
 
 
    
     
    
     
    Value
    
-    
-
-
    a liger object generated from x
    
-
-
+    
    a liger object generated from x
    
     
    
     
    
     
    References
    
-    
    modified and enhanced version of rliger::seuratToLiger.
    
+    
    modified and enhanced version of rliger::seuratToLiger.
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 liger_object <- as.LIGER(x = seurat_object)
-}
+} # }
 
-if (FALSE) {
+if (FALSE) { # \dontrun{
 liger_object <- as.LIGER(x = seurat_object_list)
-}
+} # }
 
 
    
     
    
@@ -249,15 +253,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/as.LIGER.list.html b/docs/reference/as.LIGER.list.html
new file mode 100644
index 0000000000..0f211365e0
--- /dev/null
+++ b/docs/reference/as.LIGER.list.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/as.Seurat.html b/docs/reference/as.Seurat.html
index 5284b68d43..30278ef2ca 100644
--- a/docs/reference/as.Seurat.html
+++ b/docs/reference/as.Seurat.html
@@ -1,11 +1,11 @@
 
-Convert objects to Seurat objects — as.Seurat.liger • scCustomizeConvert objects to Seurat objects — as.Seurat.liger • scCustomize
-    
+
 
     
    
       
    
 
@@ -33,7 +33,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -120,8 +126,8 @@ 
    Convert objects to Seurat objects
    
     
    
 
     
    
-    
    # S3 method for liger
-as.Seurat(
+    
    # S3 method for class 'liger'
+as.Seurat(
   x,
   nms = names(x@H),
   renormalize = TRUE,
@@ -140,74 +146,72 @@ 
    Convert objects to Seurat objects
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    liger object.
    
 
 
-
    nms
    
+
    nms
    
 
    By default, labels cell names with dataset of origin (this is to account for cells in
 different datasets which may have same name). Other names can be passed here as vector, must have
 same length as the number of datasets. (default names(H)).
    
 
 
-
    renormalize
    
+
    renormalize
    
 
    Whether to log-normalize raw data using Seurat defaults (default TRUE).
    
 
 
-
    use.liger.genes
    
+
    use.liger.genes
    
 
    Whether to carry over variable genes (default TRUE).
    
 
 
-
    by.dataset
    
+
    by.dataset
    
 
    Include dataset of origin in cluster identity in Seurat object (default FALSE).
    
 
 
-
    keep_meta
    
+
    keep_meta
    
 
    logical. Whether to transfer additional metadata (nGene/nUMI/dataset already transferred)
 to new Seurat Object.  Default is TRUE.
    
 
 
-
    reduction_label
    
+
    reduction_label
    
 
    Name of dimensionality reduction technique used.  Enables accurate transfer
 or name to Seurat object instead of defaulting to "tSNE".
    
 
 
-
    seurat_assay
    
+
    seurat_assay
    
 
    Name to set for assay in Seurat Object.  Default is "RNA".
    
 
 
-
    assay_type
    
+
    assay_type
    
 
    what type of Seurat assay to create in new object (Assay vs Assay5).
 Default is NULL which will default to the current user settings.
 See Convert_Assay parameter convert_to for acceptable values.
    
 
 
-
    add_barcode_names
    
+
    add_barcode_names
    
 
    logical, whether to add dataset names to the cell barcodes when
 creating Seurat object, default is FALSE.
    
 
 
-
    barcode_prefix
    
+
    barcode_prefix
    
 
    logical, if add_barcode_names = TRUE should the names be added as
 prefix to current cell barcodes/names or a suffix (default is TRUE; prefix).
    
 
 
-
    barcode_cell_id_delimiter
    
+
    barcode_cell_id_delimiter
    
 
    The delimiter to use when adding dataset id to barcode
 prefix/suffix.  Default is "_".
    
 
 
-
    ...
    
+
    ...
    
 
    unused.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Seurat object with raw.data, scale.data, reduction_label, iNMF, and ident slots set.
    
-
-
+    
    Seurat object with raw.data, scale.data, reduction_label, iNMF, and ident slots set.
    
 
    Seurat object.
    
     
    
     
    
@@ -223,9 +227,9 @@ 
    References
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
-seurat_object <- as.Seurat(x = liger_object)
-}
+    
    if (FALSE) { # \dontrun{
+seurat_object <- as.Seurat(x = liger_object)
+} # }
 
 
    
     
    
@@ -241,15 +245,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/as.anndata.Seurat.html b/docs/reference/as.anndata.Seurat.html
new file mode 100644
index 0000000000..1dfa81109d
--- /dev/null
+++ b/docs/reference/as.anndata.Seurat.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/as.anndata.html b/docs/reference/as.anndata.html
index 0ce3601ad6..12d33a49ab 100644
--- a/docs/reference/as.anndata.html
+++ b/docs/reference/as.anndata.html
@@ -1,9 +1,9 @@
 
-Convert objects to anndata objects — as.anndata • scCustomizeConvert objects to anndata objects — as.anndata • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -118,12 +124,12 @@ 
    Convert objects to anndata objects
    
     
    
     
    as.anndata(x, ...)
 
-# S3 method for Seurat
+# S3 method for class 'Seurat'
 as.anndata(
   x,
   file_path,
   file_name,
-  assay = "RNA",
+  assay = NULL,
   main_layer = "data",
   other_layers = "counts",
   transer_dimreduc = TRUE,
@@ -131,7 +137,7 @@ 
    Convert objects to anndata objects
    
   ...
 )
 
-# S3 method for liger
+# S3 method for class 'liger'
 as.anndata(
   x,
   file_path,
@@ -148,73 +154,73 @@ 
    Convert objects to anndata objects
    
 
     
    
     
    Arguments
    
-    
    x
    
+
+
+
    x
    
 
    Seurat or LIGER object
    
 
 
-
    ...
    
+
    ...
    
 
    Arguments passed to other methods
    
 
 
-
    file_path
    
+
    file_path
    
 
    directory file path and/or file name prefix.  Defaults to current wd.
    
 
 
-
    file_name
    
+
    file_name
    
 
    file name.
    
 
 
-
    assay
    
-
    Assay containing data to use, (default is "RNA").
    
+
    assay
    
+
    Assay containing data to use, (default is object default assay).
    
 
 
-
    main_layer
    
+
    main_layer
    
 
    the layer of data to become default layer in anndata object (default is "data").
    
 
 
-
    other_layers
    
+
    other_layers
    
 
    other data layers to transfer to anndata object (default is "counts").
    
 
 
-
    transer_dimreduc
    
+
    transer_dimreduc
    
 
    logical, whether to transfer dimensionality reduction coordinates from
 Seurat to anndata object (default is TRUE).
    
 
 
-
    verbose
    
+
    verbose
    
 
    logical, whether to print status messages during object conversion (default is TRUE).
    
 
 
-
    transfer_norm.data
    
+
    transfer_norm.data
    
 
    logical, whether to transfer the norm.data in addition to
 raw.data, default is FALSE.
    
 
 
-
    reduction_label
    
+
    reduction_label
    
 
    What to label the visualization dimensionality reduction.
 LIGER does not store name of technique and therefore needs to be set manually.
    
 
 
-
    add_barcode_names
    
+
    add_barcode_names
    
 
    logical, whether to add dataset names to the cell barcodes when
 merging object data, default is FALSE.
    
 
 
-
    barcode_prefix
    
+
    barcode_prefix
    
 
    logical, if add_barcode_names = TRUE should the names be added as
 prefix to current cell barcodes/names or a suffix (default is TRUE; prefix).
    
 
 
-
    barcode_cell_id_delimiter
    
+
    barcode_cell_id_delimiter
    
 
    The delimiter to use when adding dataset id to barcode
 prefix/suffix.  Default is "_".
    
 
 
    
     
    
     
    Value
    
-    
-
-
    an anndata object generated from x, saved at path provided.
    
+    
    an anndata object generated from x, saved at path provided.
    
     
    
     
    
     
    References
    
@@ -224,13 +230,13 @@ 
    References
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 as.anndata(x = seurat_object, file_path = "/folder_name", file_name = "anndata_converted.h5ad")
-}
+} # }
 
-if (FALSE) {
+if (FALSE) { # \dontrun{
 as.anndata(x = liger_object, file_path = "/folder_name", file_name = "anndata_converted.h5ad")
-}
+} # }
 
 
    
     
    
@@ -246,15 +252,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/as.anndata.liger.html b/docs/reference/as.anndata.liger.html
new file mode 100644
index 0000000000..1dfa81109d
--- /dev/null
+++ b/docs/reference/as.anndata.liger.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/deprecated.html b/docs/reference/deprecated.html
index 28f4ac1791..de93ab6e3e 100644
--- a/docs/reference/deprecated.html
+++ b/docs/reference/deprecated.html
@@ -1,14 +1,16 @@
 
-Deprecated functions  — Split_FeatureScatter • scCustomizeDeprecated functions  — Split_FeatureScatter • scCustomize
-    
+
 
     
    
       
    
 
@@ -36,7 +38,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -123,6 +131,8 @@ 
    Deprecated functions Add_Cell_Complexity() instead of Add_Cell_Complexity_Seurat().
    
 
    Use Add_Cell_Complexity() instead of Add_Cell_Complexity_LIGER().
    
 
    Use Meta_Present() instead of Meta_Present_LIGER().
    
+
    Use Add_Top_Gene_Pct() instead of Add_Top_Gene_Pct_Seurat().
    
+
    Use Feature_Present() instead of Gene_Present().
    
     
    
 
     
    
@@ -136,7 +146,11 @@ 
    Deprecated functions Add_Cell_Complexity_LIGER(...)
 
-Meta_Present_LIGER(...)
    
+Meta_Present_LIGER(...)
+
+Add_Top_Gene_Pct_Seurat(...)
+
+Gene_Present(...)
    
     
    
 
 
@@ -152,15 +166,15 @@ 
    Deprecated functions 
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/ensembl_hemo_id.html b/docs/reference/ensembl_hemo_id.html
new file mode 100644
index 0000000000..4172941aca
--- /dev/null
+++ b/docs/reference/ensembl_hemo_id.html
@@ -0,0 +1,181 @@
+
+Ensembl Hemo IDs — ensembl_hemo_id • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Ensembl Hemo IDs
    
+    Source: R/Data.R
+    
+    
    
+
+    
    
+    
    A list of ensembl ids for hemoglobin genes (Ensembl version 112; 4/29/2024)
    
+    
    
+
+    
    
+    
    ensembl_hemo_id
    
+    
    
+
+    
    
+    
    Format
    
+    
    A list of six vectors
    Mus_musculus_hemo_ensembl
    
+
    Ensembl IDs for mouse hemoglobin genes
    
+
+
    Homo_sapiens_hemo_ensembl
    
+
    Ensembl IDs for human hemoglobin genes
    
+
+
    Danio_rerio_hemo_ensembl
    
+
    Ensembl IDs for zebrafish hemoglobin genes
    
+
+
    Rattus_norvegicus_hemo_ensembl
    
+
    Ensembl IDs for rat hemoglobin genes
    
+
+
    Drosophila_melanogaster_hemo_ensembl
    
+
    Ensembl IDs for fly hemoglobin genes
    
+
+
    Macaca_mulatta_hemo_ensembl
    
+
    Ensembl IDs for macaque hemoglobin genes
    
+
+
    Gallus_gallus_ribo_ensembl
    
+
    Ensembl IDs for chicken hemoglobin genes
    
+
+
+
    
+    
    
+    
    Source
    
+    
    See data-raw directory for scripts used to create gene list.
    
+    
    
+
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/ensembl_ieg_list.html b/docs/reference/ensembl_ieg_list.html
new file mode 100644
index 0000000000..455e5ac478
--- /dev/null
+++ b/docs/reference/ensembl_ieg_list.html
@@ -0,0 +1,170 @@
+
+Immediate Early Gene (IEG) gene lists — ensembl_ieg_list • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Immediate Early Gene (IEG) gene lists
    
+    Source: R/Data.R
+    
+    
    
+
+    
    
+    
    Ensembl IDs for immediate early genes (Ensembl version 112; 4/29/2024)
    
+    
    
+
+    
    
+    
    ensembl_ieg_list
    
+    
    
+
+    
    
+    
    Format
    
+    
    A list of seven vectors
    Mus_musculus_IEGs
    
+
    Ensembl IDs for IEGs from source publication (see below)
    
+
+
    Homo_sapiens_IEGs
    
+
    Ensembl IDs for homologous genes from mouse gene list
    
+
+
+
+
    
+    
    
+    
    Source
    
+    
    Mouse gene list is from: SI Table 4 from doi:10.1016/j.neuron.2017.09.026
+.  Human
+gene list was compiled by first creating homologous gene list using biomaRt and then adding some manually curated
+homologs according to HGNC.  See data-raw directory for scripts used to create gene list.
    
+    
    
+
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/ensembl_mito_id.html b/docs/reference/ensembl_mito_id.html
index a74e167115..3d55a41833 100644
--- a/docs/reference/ensembl_mito_id.html
+++ b/docs/reference/ensembl_mito_id.html
@@ -1,9 +1,9 @@
 
-Ensembl Mito IDs — ensembl_mito_id • scCustomizeEnsembl Mito IDs — ensembl_mito_id • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -112,7 +118,7 @@ 
    Ensembl Mito IDs
    
     
    
 
     
    
-    
    A list of ensembl ids for mitochondrial genes (Ensembl version 105)
    
+    
    A list of ensembl ids for mitochondrial genes (Ensembl version 112; 4/29/2024)
    
     
    
 
     
    
@@ -139,9 +145,15 @@ 
    Format
    
 
    Macaca_mulatta_mito_ensembl
    
 
    Ensembl IDs for macaque mitochondrial genes
    
 
+
    Gallus_gallus_ribo_ensembl
    
+
    Ensembl IDs for chicken mitochondrial genes
    
 
 
 
    
+    
    
+    
    Source
    
+    
    See data-raw directory for scripts used to create gene list.
    
+    
    
 
   
    
   
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/ensembl_ribo_id.html b/docs/reference/ensembl_ribo_id.html
index d45e742081..acd85eac7e 100644
--- a/docs/reference/ensembl_ribo_id.html
+++ b/docs/reference/ensembl_ribo_id.html
@@ -1,9 +1,9 @@
 
-Ensembl Ribo IDs — ensembl_ribo_id • scCustomizeEnsembl Ribo IDs — ensembl_ribo_id • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -112,7 +118,7 @@ 
    Ensembl Ribo IDs
    
     
    
 
     
    
-    
    A list of ensembl ids for ribosomal genes (Ensembl version 105)
    
+    
    A list of ensembl ids for ribosomal genes (Ensembl version 112; 4/29/2024)
    
     
    
 
     
    
@@ -121,7 +127,7 @@ 
    Ensembl Ribo IDs
    
 
     
    
     
    Format
    
-    
    A list of seven vectors
    Mus_musculus_ribo_ensembl
    
+    
    A list of eight vectors
    Mus_musculus_ribo_ensembl
    
 
    Ensembl IDs for mouse ribosomal genes
    
 
 
    Homo_sapiens_ribo_ensembl
    
@@ -142,9 +148,15 @@ 
    Format
    
 
    Macaca_mulatta_ribo_ensembl
    
 
    Ensembl IDs for macaque ribosomal genes
    
 
+
    Gallus_gallus_ribo_ensembl
    
+
    Ensembl IDs for chicken ribosomal genes
    
 
 
 
    
+    
    
+    
    Source
    
+    
    See data-raw directory for scripts used to create gene list.
    
+    
    
 
   
    
   
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/ieg_gene_list.html b/docs/reference/ieg_gene_list.html
index fd972ecb55..96c1112154 100644
--- a/docs/reference/ieg_gene_list.html
+++ b/docs/reference/ieg_gene_list.html
@@ -1,9 +1,9 @@
 
-Immediate Early Gene (IEG) gene lists — ieg_gene_list • scCustomizeImmediate Early Gene (IEG) gene lists — ieg_gene_list • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -135,7 +141,7 @@ 
    Source
    
     
    Mouse gene list is from: SI Table 4 from doi:10.1016/j.neuron.2017.09.026
 .  Human
 gene list was compiled by first creating homologous gene list using biomaRt and then adding some manually curated
-homologs according to HGNC.
    
+homologs according to HGNC.  See data-raw directory for scripts used to create gene list.
    
     
    
 
   
    
@@ -150,15 +156,15 @@ 
    Source
    
 
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 6a357d1c70..2ebea55848 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,9 +1,9 @@
 
-Function reference • scCustomizePackage index • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -161,6 +167,10 @@ 
    Read & Write Data Read_Metrics_10X() 
    
         
         
    
+      
+        
+      
+        
@@ -425,6 +439,10 @@ 
    LIGER Plotting Functions DimPlot_LIGER() 
    
         
         
    
+      
+        
@@ -513,12 +531,16 @@ 
    QC Utilities Add_Cell_QC_Metrics() 
    
         
         
    
+      
+        
+      
+        
+      
+        
@@ -560,8 +590,7 @@ 
    Check Utilities Case_Check() 
    
         
-        
    
+        
@@ -570,10 +599,6 @@ 
    Check Utilities Feature_Present() 
    
         
         
    
-      
-        
@@ -602,6 +627,14 @@ 
    Misc Utilities Updated_HGNC_Symbols() 
    
         
         
    
+      
+        
+      
+        
+      
+        
+      
+        
+      
+        
+      
+        
-        
+        
+      
+        
+      
+        
@@ -630,6 +687,10 @@ 
    Helper Utilities (LIGER) Variable_Features_ALL_LIGER() 
    
         
         
    
+      
+        
-        
+        
+      
+        
@@ -746,11 +811,23 @@ 
    Statistics Functions Plot_Median_UMIs() 
    
         
         
    
+      
+        
+        
+      
+        
+      
@@ -762,6 +839,10 @@ 
    Data 
    ieg_gene_list 
    
+      
+        
@@ -779,15 +860,15 @@ 
    Data 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/msigdb_qc_ensembl_list.html b/docs/reference/msigdb_qc_ensembl_list.html
new file mode 100644
index 0000000000..c6587b4969
--- /dev/null
+++ b/docs/reference/msigdb_qc_ensembl_list.html
@@ -0,0 +1,227 @@
+
+QC Gene Lists — msigdb_qc_ensembl_list • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    QC Gene Lists
    
+    Source: R/Data.R
+    
+    
    
+
+    
    
+    
    Ensembl IDs for qc percentages from MSigDB database.  The gene sets are from 3 MSigDB lists:
+"HALLMARK_OXIDATIVE_PHOSPHORYLATION", "HALLMARK_APOPTOSIS", and "HALLMARK_DNA_REPAIR".
+(Ensembl version 112; 4/29/2024)
    
+    
    
+
+    
    
+    
    msigdb_qc_ensembl_list
    
+    
    
+
+    
    
+    
    Format
    
+    
    A list of 21 vectors
    Homo_sapiens_msigdb_oxphos
    
+
    Genes in msigdb "HALLMARK_OXIDATIVE_PHOSPHORYLATION" list for human
    
+
+
    Homo_sapiens_msigdb_apop
    
+
    Genes in msigdb "HALLMARK_APOPTOSIS" list for human
    
+
+
    Homo_sapiens_msigdb_dna_repair
    
+
    Genes in msigdb "HALLMARK_DNA_REPAIR" list for human
    
+
+
    Mus_musculus_msigdb_oxphos
    
+
    Genes in msigdb "HALLMARK_OXIDATIVE_PHOSPHORYLATION" list for mouse
    
+
+
    Mus_musculus_msigdb_apop
    
+
    Genes in msigdb "HALLMARK_APOPTOSIS" list for mouse
    
+
+
    Mus_musculus_msigdb_dna_repair
    
+
    Genes in msigdb "HALLMARK_DNA_REPAIR" list for mouse
    
+
+
    Rattus_norvegicus_msigdb_oxphos
    
+
    Genes in msigdb "HALLMARK_OXIDATIVE_PHOSPHORYLATION" list for rat
    
+
+
    Rattus_norvegicus_msigdb_apop
    
+
    Genes in msigdb "HALLMARK_APOPTOSIS" list for rat
    
+
+
    Rattus_norvegicus_msigdb_dna_repair
    
+
    Genes in msigdb "HALLMARK_DNA_REPAIR" list for rat
    
+
+
    Drosophila_melanogaster_msigdb_oxphos
    
+
    Genes in msigdb "HALLMARK_OXIDATIVE_PHOSPHORYLATION" list for fly
    
+
+
    Drosophila_melanogaster_msigdb_apop
    
+
    Genes in msigdb "HALLMARK_APOPTOSIS" list for fly
    
+
+
    Drosophila_melanogaster_msigdb_dna_repair
    
+
    Genes in msigdb "HALLMARK_DNA_REPAIR" list for fly
    
+
+
    Dario_rerio_msigdb_oxphos
    
+
    Genes in msigdb "HALLMARK_OXIDATIVE_PHOSPHORYLATION" list for zebrafish
    
+
+
    Dario_rerio_msigdb_apop
    
+
    Genes in msigdb "HALLMARK_APOPTOSIS" list for zebrafish
    
+
+
    Dario_rerio_msigdb_dna_repair
    
+
    Genes in msigdb "HALLMARK_DNA_REPAIR" list for zebrafish
    
+
+
    Macaca_mulatta_msigdb_oxphos
    
+
    Genes in msigdb "HALLMARK_OXIDATIVE_PHOSPHORYLATION" list for macaque
    
+
+
    Macaca_mulatta_msigdb_apop
    
+
    Genes in msigdb "HALLMARK_APOPTOSIS" list for macaque
    
+
+
    Macaca_mulatta_msigdb_dna_repair
    
+
    Genes in msigdb "HALLMARK_DNA_REPAIR" list for macaque
    
+
+
    Gallus_gallus_msigdb_oxphos
    
+
    Genes in msigdb "HALLMARK_OXIDATIVE_PHOSPHORYLATION" list for chicken
    
+
+
    Gallus_gallus_msigdb_apop
    
+
    Genes in msigdb "HALLMARK_APOPTOSIS" list for chicken
    
+
+
    Gallus_gallus_msigdb_dna_repair
    
+
    Genes in msigdb "HALLMARK_DNA_REPAIR" list for chicken
    
+
+
+
    
+    
    
+    
    Source
    
+    
    MSigDB gene sets (ensembl IDs) via msigdbr package https://cran.r-project.org/package=msigdbr.  See data-raw directory for scripts used to create gene list.
    
+    
    
+
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/msigdb_qc_gene_list.html b/docs/reference/msigdb_qc_gene_list.html
index 293799e861..3be6e387ad 100644
--- a/docs/reference/msigdb_qc_gene_list.html
+++ b/docs/reference/msigdb_qc_gene_list.html
@@ -1,10 +1,10 @@
 
-QC Gene Lists — msigdb_qc_gene_list • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
 
-      
+
 
       
    
   
    
@@ -123,7 +129,7 @@ 
    QC Gene Lists
    
 
     
    
     
    Format
    
-    
    A list of 18 vectors
    Homo_sapiens_msigdb_oxphos
    
+    
    A list of 21 vectors
    Homo_sapiens_msigdb_oxphos
    
 
    Genes in msigdb "HALLMARK_OXIDATIVE_PHOSPHORYLATION" list for human
    
 
 
    Homo_sapiens_msigdb_apop
    
@@ -177,12 +183,20 @@ 
    Format
    
 
    Macaca_mulatta_msigdb_dna_repair
    
 
    Genes in msigdb "HALLMARK_DNA_REPAIR" list for macaque
    
 
+
    Gallus_gallus_msigdb_oxphos
    
+
    Genes in msigdb "HALLMARK_OXIDATIVE_PHOSPHORYLATION" list for chicken
    
+
+
    Gallus_gallus_msigdb_apop
    
+
    Genes in msigdb "HALLMARK_APOPTOSIS" list for chicken
    
+
+
    Gallus_gallus_msigdb_dna_repair
    
+
    Genes in msigdb "HALLMARK_DNA_REPAIR" list for chicken
    
 
 
 
    
     
    
     
    Source
    
-    
    MSigDB gene sets via msigdbr package https://cran.r-project.org/package=msigdbr
    
+    
    MSigDB gene sets (gene symbols) via msigdbr package https://cran.r-project.org/package=msigdbr.  See data-raw directory for scripts used to create gene list.
    
     
    
 
   
    
@@ -197,15 +211,15 @@ 
    Source
    
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/plotFactors_scCustom.html b/docs/reference/plotFactors_scCustom.html
index 8cdb78bddf..3658aa909f 100644
--- a/docs/reference/plotFactors_scCustom.html
+++ b/docs/reference/plotFactors_scCustom.html
@@ -1,9 +1,9 @@
 
-Customized version of plotFactors — plotFactors_scCustom • scCustomizeCustomized version of plotFactors — plotFactors_scCustom • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
 
-      
+
 
       
    
   
    
@@ -123,6 +129,7 @@ 
    Customized version of plotFactors
    
   colors_use_dimreduc = c("lemonchiffon", "red"),
   pt.size_factors = 1,
   pt.size_dimreduc = 1,
+  reduction = "UMAP",
   reduction_label = "UMAP",
   plot_legend = TRUE,
   raster = TRUE,
@@ -142,100 +149,106 @@ 
    Customized version of plotFactors
    
 
     
    
     
    Arguments
    
-    
    liger_object
    
+
+
+
    liger_object
    
 
    liger liger_object.  Need to perform clustering and factorization before calling this function
    
 
 
-
    num_genes
    
+
    num_genes
    
 
    Number of genes to display for each factor (Default 8).
    
 
 
-
    colors_use_factors
    
+
    colors_use_factors
    
 
    colors to use for plotting factor loadings  By default datasets will be
 plotted using "varibow" with shuffle = TRUE from both from DiscretePalette_scCustomize.
    
 
 
-
    colors_use_dimreduc
    
+
    colors_use_dimreduc
    
 
    colors to use for plotting factor loadings on dimensionality reduction
 coordinates (tSNE/UMAP).  Default is c('lemonchiffon', 'red'),
    
 
 
-
    pt.size_factors
    
+
    pt.size_factors
    
 
    Adjust point size for plotting in the factor plots.
    
 
 
-
    pt.size_dimreduc
    
+
    pt.size_dimreduc
    
 
    Adjust point size for plotting in dimensionality reduction plots.
    
 
 
-
    reduction_label
    
+
    reduction
    
+
    Name of dimensionality reduction to use for plotting.  Default is "UMAP".
+Only for newer style liger objects.
    
+
+
+
    reduction_label
    
 
    What to label the x and y axes of resulting plots.  LIGER does not store name of
-technique and therefore needs to be set manually.  Default is "UMAP".
    
+technique and therefore needs to be set manually.  Default is "UMAP".
+Only for older style liger objects.
    
 
 
-
    plot_legend
    
+
    plot_legend
    
 
    logical, whether to plot the legend on factor loading plots, default is TRUE.
 Helpful if number of datasets is large to avoid crowding the plot with legend.
    
 
 
-
    raster
    
+
    raster
    
 
    Convert points to raster format.  Default is NULL which will rasterize by default if
 greater than 200,000 cells.
    
 
 
-
    raster.dpi
    
+
    raster.dpi
    
 
    Pixel resolution for rasterized plots, passed to geom_scattermore().
 Default is c(512, 512).
    
 
 
-
    order
    
+
    order
    
 
    logical. Whether to plot higher loading cells on top of cells with lower loading values in the
 dimensionality reduction plots (Default = FALSE).
    
 
 
-
    plot_dimreduc
    
+
    plot_dimreduc
    
 
    logical.  Whether to plot factor loadings on dimensionality reduction coordinates.  Default is TRUE.
    
 
 
-
    save_plots
    
+
    save_plots
    
 
    logical.  Whether to save plots.  Default is TRUE
    
 
 
-
    file_path
    
+
    file_path
    
 
    directory file path and/or file name prefix.  Defaults to current wd.
    
 
 
-
    file_name
    
+
    file_name
    
 
    name suffix to append after sample name.
    
 
 
-
    return_plots
    
+
    return_plots
    
 
    logical. Whether or not to return plots to the environment.  (Default is FALSE)
    
 
 
-
    cells.highlight
    
+
    cells.highlight
    
 
    Names of specific cells to highlight in plot (black) (default NULL).
    
 
 
-
    reorder_datasets
    
+
    reorder_datasets
    
 
    New order to plot datasets in for the factor plots if different from current
-factor level order in cell.data slot.
    
+factor level order in cell.data slot. Only for older style liger objects.
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  If colors_use_factors = NULL, Whether or not to return plot using
 default ggplot2 "hue" palette instead of default "varibow" palette.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed for the palette shuffle if colors_use_factors = NULL.  Default = 123.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    A list of ggplot/patchwork objects and/or PDF file.
    
+    
    A list of ggplot/patchwork objects and/or PDF file.
    
     
    
     
    
     
    References
    
@@ -248,10 +261,10 @@ 
    Author
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 plotFactors_scCustom(liger_object = liger_obj, return_plots = FALSE, plot_dimreduc = TRUE,
 raster = FALSE, save_plots = TRUE)
-}
+} # }
 
 
    
     
    
@@ -267,15 +280,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html
index cfa559ff46..7a256757dc 100644
--- a/docs/reference/reexports.html
+++ b/docs/reference/reexports.html
@@ -1,16 +1,16 @@
 
-Objects exported from other packages — reexports • scCustomizeObjects exported from other packages — reexports • scCustomize
-    
+
 
     
    
       
    
 
@@ -38,7 +38,7 @@
 
  • 
   
   
    • 
   
    
 
    
 
-      
+
 
       
    
   
    
@@ -122,7 +128,7 @@ 
    Objects exported from other packages
    
     
    These objects are imported from other packages. Follow the links
 below to see their documentation.
    
 
    SeuratObject
    
-
    as.Seurat
    
+
    as.Seurat, Cells, Embeddings, Features, Idents, Idents<-, WhichCells
    
 
 
 
    
@@ -131,6 +137,12 @@ 
    Objects exported from other packages
    
     
    
     
    Note
    
     
    See as.Seurat.liger for scCustomize extension of this generic to converting Liger objects.
    
+
    See WhichCells.liger for scCustomize extension of this generic to extract cell barcodes.
    
+
    See Cells.liger for scCustomize extension of this generic to extract cell barcodes.
    
+
    See Features.liger for scCustomize extension of this generic to extract dataset features.
    
+
    See Embeddings.liger for scCustomize extension of this generic to extract embeddings.
    
+
    See Idents.liger for scCustomize extension of this generic to extract cell identities.
    
+
    See Idents.liger for scCustomize extension of this generic to set cell identities.
    
     
    
 
   
    
@@ -145,15 +157,15 @@ 
    Note
    
 
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/scCustomize-package.html b/docs/reference/scCustomize-package.html
index 1851baf7ec..0810cdcdc5 100644
--- a/docs/reference/scCustomize-package.html
+++ b/docs/reference/scCustomize-package.html
@@ -1,10 +1,10 @@
 
-scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing — scCustomize-package • scCustomizescCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing — scCustomize-package • scCustomize
-    
+
 
     
    
       
    
 
@@ -32,7 +32,7 @@
 
  • 
   
   
    • 
   
 
 
-      
+
 
       
    
   
    
@@ -120,7 +126,7 @@ 
    scCustomize: Custom Visualizations & Functions for Streamlined Analyses
 
     
    
     
    Package options
    
-    
+
 
 
 
    scCustomize uses the following options() to configure behavior:
    
@@ -193,15 +199,15 @@ 
    Author
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/scCustomize.html b/docs/reference/scCustomize.html
new file mode 100644
index 0000000000..4cb99c7a76
--- /dev/null
+++ b/docs/reference/scCustomize.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/scCustomize_Palette-1.png b/docs/reference/scCustomize_Palette-1.png
index a1cb6bb6a9..d21fe12415 100644
Binary files a/docs/reference/scCustomize_Palette-1.png and b/docs/reference/scCustomize_Palette-1.png differ
diff --git a/docs/reference/scCustomize_Palette.html b/docs/reference/scCustomize_Palette.html
index 582f41c391..f1aa9fdfde 100644
--- a/docs/reference/scCustomize_Palette.html
+++ b/docs/reference/scCustomize_Palette.html
@@ -1,9 +1,9 @@
 
-Color Palette Selection for scCustomize — scCustomize_Palette • scCustomizeColor Palette Selection for scCustomize — scCustomize_Palette • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -125,26 +131,26 @@ 
    Color Palette Selection for scCustomize
    
 
     
    
     
    Arguments
    
-    
    num_groups
    
+
+
+
    num_groups
    
 
    number of groups to be plotted. If ggplot_default_colors = FALSE then by default:
    • If number of levels plotted equal to 2 then colors will be NavyAndOrange().
      • 
 
    • If number of levels plotted greater than 2 but less than or equal to 36 it will use "polychrome" from DiscretePalette_scCustomize().
      • 
 
    • If greater than 36 will use "varibow" with shuffle = TRUE from DiscretePalette_scCustomize.
      • 
 
    
 
 
-
    ggplot_default_colors
    
+
    ggplot_default_colors
    
 
    logical.  Whether to use default ggplot hue palette or not.
    
 
 
-
    color_seed
    
+
    color_seed
    
 
    random seed to use for shuffling the "varibow" palette.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    vector of colors to use for plotting.
    
+    
    vector of colors to use for plotting.
    
     
    
 
     
    
@@ -167,15 +173,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/seq_zeros.html b/docs/reference/seq_zeros.html
new file mode 100644
index 0000000000..5292f0b965
--- /dev/null
+++ b/docs/reference/seq_zeros.html
@@ -0,0 +1,197 @@
+
+Create sequence with zeros — seq_zeros • scCustomize
+
+
+    
    
+      
    
+
+
+
+      
    
+  
    
+    
    
+    
    Create sequence with zeros
    
+    Source: R/Utilities.R
+    
+    
    
+
+    
    
+    
    Create sequences of numbers like seq() or seq_len() but with zeros prefixed to
+keep numerical order
    
+    
    
+
+    
    
+    
    seq_zeros(seq_length, num_zeros = NULL)
    
+    
    
+
+    
    
+    
    Arguments
    
+
+
+
    seq_length
    
+
    a seqeunce or numbers of numbers to create sequence.
+Users can provide sequence (1:XX) or number of values to add in sequence (will
+be used as second number in seq_len; 1:XX).
    
+
+
+
    num_zeros
    
+
    number of zeros to prefix sequence, default is  (e.g, 01, 02, 03, ...)
    
+
+
    
+    
    
+    
    Value
    
+    
    vector of numbers in sequence
    
+    
    
+    
    
+    
    References
    
+    
    Base code from stackoverflow post:
+https://stackoverflow.com/a/38825614
    
+    
    
+
+    
    
+    
    Examples
    
+    
    # Using sequence
+new_seq <- seq_zeros(seq_length = 1:15, num_zeros = 1)
+new_seq
+#>  [1] "01" "02" "03" "04" "05" "06" "07" "08" "09" "10" "11" "12" "13" "14" "15"
+
+# Using number
+new_seq <- seq_zeros(seq_length = 15, num_zeros = 1)
+new_seq
+#>  [1] "01" "02" "03" "04" "05" "06" "07" "08" "09" "10" "11" "12" "13" "14" "15"
+
+# Sequence with 2 zeros
+new_seq <- seq_zeros(seq_length = 1:15, num_zeros = 2)
+new_seq
+#>  [1] "001" "002" "003" "004" "005" "006" "007" "008" "009" "010" "011" "012"
+#> [13] "013" "014" "015"
+
+
    
+    
    
+  
    
+  
+
    
+
+
+      
    
+  
    Developed by Samuel Marsh.
    
+
    
+
+
    
+  
    Site built with pkgdown 2.1.0.
    
+
    
+
+      
    
+
+
+
+
+
+
+  
+
diff --git a/docs/reference/theme_ggprism_mod-1.png b/docs/reference/theme_ggprism_mod-1.png
index 09698702ac..5e123896d9 100644
Binary files a/docs/reference/theme_ggprism_mod-1.png and b/docs/reference/theme_ggprism_mod-1.png differ
diff --git a/docs/reference/theme_ggprism_mod.html b/docs/reference/theme_ggprism_mod.html
index a15e8b2193..1511397cef 100644
--- a/docs/reference/theme_ggprism_mod.html
+++ b/docs/reference/theme_ggprism_mod.html
@@ -1,9 +1,9 @@
 
-Modified ggprism theme — theme_ggprism_mod • scCustomizeModified ggprism theme — theme_ggprism_mod • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -130,46 +136,46 @@ 
    Modified ggprism theme
    
 
     
    
     
    Arguments
    
-    
    palette
    
+
+
+
    palette
    
 
    string. Palette name, use
 names(ggprism_data$themes) to show all valid palette names.
    
 
 
-
    base_size
    
+
    base_size
    
 
    numeric. Base font size, given in "pt".
    
 
 
-
    base_family
    
+
    base_family
    
 
    string. Base font family, default is "sans".
    
 
 
-
    base_fontface
    
+
    base_fontface
    
 
    string. Base font face, default is "bold".
    
 
 
-
    base_line_size
    
+
    base_line_size
    
 
    numeric. Base linewidth for line elements
    
 
 
-
    base_rect_size
    
+
    base_rect_size
    
 
    numeric. Base linewidth for rect elements
    
 
 
-
    axis_text_angle
    
+
    axis_text_angle
    
 
    integer. Angle of axis text in degrees.
 One of: 0, 45, 90, 270.
    
 
 
-
    border
    
+
    border
    
 
    logical. Should a border be drawn around the plot?
 Clipping will occur unless e.g. coord_cartesian(clip = "off") is used.
    
 
 
    
     
    
     
    Value
    
-    
-
-
    Returns a list-like object of class theme.
    
+    
    Returns a list-like object of class theme.
    
     
    
     
    
     
    References
    
@@ -202,15 +208,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/reference/viridis_dark_high.html b/docs/reference/viridis_dark_high.html
new file mode 100644
index 0000000000..aa26f7eb9f
--- /dev/null
+++ b/docs/reference/viridis_dark_high.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/viridis_inferno_dark_high.html b/docs/reference/viridis_inferno_dark_high.html
new file mode 100644
index 0000000000..aa26f7eb9f
--- /dev/null
+++ b/docs/reference/viridis_inferno_dark_high.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/viridis_inferno_light_high.html b/docs/reference/viridis_inferno_light_high.html
new file mode 100644
index 0000000000..aa26f7eb9f
--- /dev/null
+++ b/docs/reference/viridis_inferno_light_high.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/viridis_light_high.html b/docs/reference/viridis_light_high.html
new file mode 100644
index 0000000000..aa26f7eb9f
--- /dev/null
+++ b/docs/reference/viridis_light_high.html
@@ -0,0 +1,8 @@
+
+  
+    
+    
+    
+  
+
+
diff --git a/docs/reference/viridis_magma_dark_high.html b/docs/reference/viridis_magma_dark_high.html
new file mode 100644
index 0000000000..aa26f7eb9f
--- /dev/null
+++ b/docs/reference/viridis_magma_dark_high.html
@@ -0,0 +1,8 @@
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diff --git a/docs/reference/viridis_magma_light_high.html b/docs/reference/viridis_magma_light_high.html
new file mode 100644
index 0000000000..aa26f7eb9f
--- /dev/null
+++ b/docs/reference/viridis_magma_light_high.html
@@ -0,0 +1,8 @@
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diff --git a/docs/reference/viridis_plasma_light_high.html b/docs/reference/viridis_plasma_light_high.html
new file mode 100644
index 0000000000..aa26f7eb9f
--- /dev/null
+++ b/docs/reference/viridis_plasma_light_high.html
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diff --git a/docs/reference/viridis_shortcut.html b/docs/reference/viridis_shortcut.html
index 8770837bc2..4745ce1b35 100644
--- a/docs/reference/viridis_shortcut.html
+++ b/docs/reference/viridis_shortcut.html
@@ -1,9 +1,9 @@
 
-Viridis Shortcuts — viridis_plasma_dark_high • scCustomizeViridis Shortcuts — viridis_plasma_dark_high • scCustomize
-    
+
 
     
    
       
    
 
@@ -31,7 +31,7 @@
 
  • 
   
   
    • 
   
    
 
 
-      
+
 
       
    
   
    
@@ -146,17 +152,15 @@ 
    Format
    
     
    
     
    
     
    Value
    
-    
-
-
    A color palette for plotting
    
+    
    A color palette for plotting
    
     
    
 
     
    
     
    Examples
    
-    
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 FeaturePlot_scCustom(object = seurat_object, features = "Cx3cr1",
 colors_use = viridis_plasma_dark_high, na_color = "lightgray")
-}
+} # }
 
 
    
     
    
@@ -172,15 +176,15 @@ 
    Examples
    
 
    
 
 
    
-  
    Site built with pkgdown 2.0.7.
    
+  
    Site built with pkgdown 2.1.0.
    
 
    
 
       
    
 
-  
 
 
-  
+
+
 
   
 
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 4c62db13ad..2a88cf2e95 100644
--- a/docs/sitemap.xml
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+https://samuel-marsh.github.io/scCustomize/reference/Updated_MGI_Symbols.html
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+https://samuel-marsh.github.io/scCustomize/reference/scCustomize_Palette.html
+https://samuel-marsh.github.io/scCustomize/reference/seq_zeros.html
+https://samuel-marsh.github.io/scCustomize/reference/theme_ggprism_mod.html
+https://samuel-marsh.github.io/scCustomize/reference/viridis_shortcut.html
 
+
diff --git a/inst/pkgdown.yml b/inst/pkgdown.yml
index 084ef83a15..52153f2c14 100644
--- a/inst/pkgdown.yml
+++ b/inst/pkgdown.yml
@@ -1,25 +1,26 @@
-pandoc: 3.1.4
-pkgdown: 2.0.7
+pandoc: '3.2'
+pkgdown: 2.1.0
 pkgdown_sha: ~
 articles:
-  Cell_Bender_Functions: Cell_Bender_Functions.html
-  Color_Palettes: Color_Palettes.html
-  FAQ: FAQ.html
-  Gene_Expression_Plotting: Gene_Expression_Plotting.html
-  Helpers_and_Utilities: Helpers_and_Utilities.html
-  Installation: Installation.html
-  Iterative_Plotting: Iterative_Plotting.html
-  LIGER_Functions: LIGER_Functions.html
-  Markers_and_Cluster_Annotation: Markers_and_Cluster_Annotation.html
-  Misc_Functions: Misc_Functions.html
-  Object_Conversion: Object_Conversion.html
-  QC_Plots: QC_Plots.html
-  Read_and_Write_Functions: Read_and_Write_Functions.html
-  Sequencing_QC_Plots: Sequencing_QC_Plots.html
-  Statistics: Statistics.html
-  Update_Gene_Symbols: Update_Gene_Symbols.html
-last_built: 2024-02-28T19:49Z
+  articles/Cell_Bender_Functions: Cell_Bender_Functions.html
+  articles/Color_Palettes: Color_Palettes.html
+  articles/FAQ: FAQ.html
+  articles/Gene_Expression_Plotting: Gene_Expression_Plotting.html
+  articles/Helpers_and_Utilities: Helpers_and_Utilities.html
+  articles/Installation: Installation.html
+  articles/Iterative_Plotting: Iterative_Plotting.html
+  articles/LIGER_Functions: LIGER_Functions.html
+  articles/Markers_and_Cluster_Annotation: Markers_and_Cluster_Annotation.html
+  articles/Misc_Functions: Misc_Functions.html
+  articles/Object_Conversion: Object_Conversion.html
+  articles/Object_QC_Functions: Object_QC_Functions.html
+  articles/QC_Plots: QC_Plots.html
+  articles/Read_and_Write_Functions: Read_and_Write_Functions.html
+  articles/Sequencing_QC_Plots: Sequencing_QC_Plots.html
+  articles/Spatial_Plotting: Spatial_Plotting.html
+  articles/Statistics: Statistics.html
+  articles/Update_Gene_Symbols: Update_Gene_Symbols.html
+last_built: 2024-12-05T19:28Z
 urls:
   reference: https://samuel-marsh.github.io/scCustomize/reference
   article: https://samuel-marsh.github.io/scCustomize/articles
-

    
 
    
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-11.69341
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    Read Overall Statistics from 10X Cell Ranger Count
    
+          
    Read_Metrics_CellBender() 
    
+        
    Read Overall Statistics from CellBender
    		
       
    
           
    Merge Data Utilities 
    
           
    Utilities to merge raw data.
    
@@ -361,6 +371,10 @@ 
    Seurat Plotting Functions PC_Plotting() 
    
         
         
    PC Plots
    
+          
    SpatialDimPlot_scCustom() 
    
+        
    SpatialDimPlot with modified default settings
    		
       
    
           
    Stacked_VlnPlot() 
    
         
    DimPlot LIGER Version
    
+          
    Factor_Cor_Plot() 
    
+        
    Factor Correlation Plot
    		
       
    
           
    plotFactors_scCustom() 
    
         
    Add Multiple Cell Quality Control Values with Single Function
    
+          
    Add_Hemo() 
    
+        
    Add Hemoglobin percentages
    		
       
    
           
    Add_Mito_Ribo() 
    
             		
         
    Add Mito and Ribo percentages
    		
       
    
-          
    Add_Top_Gene_Pct_Seurat() 
    
+          
    Add_Top_Gene_Pct() 
    
             		
         
    Add Percent of High Abundance Genes
    		
       
    
@@ -545,6 +567,14 @@ 
    Getters/Setters Meta_Remove_Seurat() 
    
         
         
    Remove meta data columns containing Seurat Defaults
    
+          
    Random_Cells_Downsample() 
    
+        
    Randomly downsample by identity
    
+          
    Rename_Clusters() 
    
+        
    Rename Clusters
    		
       
    
           
    Store_Misc_Info_Seurat() 
    
         
    Check for alternate case features
-Checks Seurat object for the presence of features with the same spelling but alternate case.
    Check for alternate case features
    		
       
    
           
    CheckMatrix_scCustom() 
    
         
    Check if genes/features are present
    
-          
    Gene_Present() 
    
-        
    Check if genes/features are present  [Soft-deprecated]
    		
       
    
           
    Meta_Numeric() 
    
         
    Update HGNC Gene Symbols
    
+          
    Updated_MGI_Symbols() 
    
+        
    Update MGI Gene Symbols
    
+          
    seq_zeros() 
    
+        
    Create sequence with zeros
    		
       
    
           
    Helper Utilities (LIGER) 
    
           
    Functions to provide ease of use for frequently used code from LIGER Objects.
    
@@ -614,14 +647,38 @@ 
    Helper Utilities (LIGER) Add_Mito_Ribo() 
    
         
         
    Add Mito and Ribo percentages
    
+          
    Cells(<liger>) 
    
+        
    Extract Cells from LIGER Object
    
+          
    Cells_by_Identities_LIGER() 
    
+        
    Extract Cells by identity
    
+          
    Embeddings(<liger>) 
    
+        
    Extract matrix of embeddings
    
+          
    Features(<liger>) 
    
+        
    Extract Features from LIGER Object
    		
       
    
           
    Fetch_Meta() 
    
             		
         
    Get meta data from object
    		
       
    
-          
    LIGER_Features() 
    
+          
    Find_Factor_Cor() 
    
         
    Extract Features from LIGER Object
    Find Factor Correlations
    
+          
    Idents(<liger>) `Idents<-`(<liger>) 
    
+        
    Extract or set default identities from object
    
+          
    Subset_LIGER() 
    
+        
    Subset LIGER object
    		
       
    
           
    Top_Genes_Factor() 
    
         
    Perform variable gene selection over whole dataset
    
+          
    WhichCells(<liger>) 
    
+        
    Extract Cells for particular identity
    		
       
    
           
    Object Conversion Functions 
    
           
    Functions to convert between different single cell object formats (R & Python).
    
@@ -681,7 +742,7 @@ 
    Cluster/Marker Annotation Utilities
       
    
           
    Rename_Clusters() 
    
         
    Rename Cluster Seurat
    Rename Clusters
    		
       
    
           
    Project Organization Utilities 
    
           
    Functions to provide ease of use for organization of analysis projects.
    
@@ -706,6 +767,10 @@ 
    Statistics Functions CellBender_Feature_Diff() 
    
         
         
    CellBender Feature Differences
    
+          
    Cells_per_Sample() 
    
+        
    Cells per Sample
    		
       
    
           
    Cluster_Stats_All_Samples() 
    
         
    Plot Median UMIs per Cell per Sample
    
+          
    Proportion_Plot() 
    
+        
    Cell Proportion Plot
    		
       
    
           
    Data 
    
           
    Reference data for package functions.
    
             		
       
    
+          
    ensembl_hemo_id 
    
+        
    Ensembl Hemo IDs
    
+          
    ensembl_ieg_list 
    
+        
    Immediate Early Gene (IEG) gene lists
    
           
    ensembl_mito_id 
    
             		
         
    Ensembl Mito IDs
    		
           
         
         
    Immediate Early Gene (IEG) gene lists
    
+          
    msigdb_qc_ensembl_list 
    
+        
    QC Gene Lists
    		
       
    
           
    msigdb_qc_gene_list