diff --git a/404.html b/404.html index 616e69f9..490b218a 100644 --- a/404.html +++ b/404.html @@ -33,7 +33,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/LICENSE-text.html b/LICENSE-text.html index 11487abd..b00472de 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/articles/index.html b/articles/index.html index 8df6e038..d2d3e6ed 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/articles/miaViz.html b/articles/miaViz.html index 84537a3e..7ce92689 100644 --- a/articles/miaViz.html +++ b/articles/miaViz.html @@ -34,7 +34,7 @@ miaViz - 1.9.2 + 1.9.3 @@ -94,8 +94,8 @@

Installation#> Warning: package(s) not installed when version(s) same as or greater than current; use #> `force = TRUE` to re-install: 'miaViz' #> Old packages: 'basilisk', 'basilisk.utils', 'densvis', 'dir.expiry', -#> 'TreeSummarizedExperiment', 'KernSmooth', 'Matrix', 'mgcv', 'nlme', -#> 'spatial', 'survival' +#> 'TreeSummarizedExperiment', 'tinytex', 'foreign', 'KernSmooth', 'lattice', +#> 'Matrix', 'mgcv', 'nlme', 'spatial', 'survival' 
 library(miaViz)
 data(GlobalPatterns, package = "mia")
@@ -396,62 +396,29 @@

Serial data ordination and traj }

Principal Coordinates Analysis using Bray-Curtis dissimilarity on the hitchip1006 dataset:

-

Retrieving information about all available trajectories:

+library(miaTime)
+data(hitchip1006, package = "miaTime")
+tse <- hitchip1006
+tse <- transformAssay(tse, method = "relabundance")
+## Ordination with PCoA with Bray-Curtis dissimilarity
+tse <- runMDS(tse, FUN = vegan::vegdist, method = "bray", name = "PCoA_BC",
+              assay.type = "relabundance", na.rm = TRUE)
+# plot
+p <- plotReducedDim(tse, dimred = "PCoA_BC")
+p
+

Retrieving information about all available trajectories:

+
 library(dplyr)
-#> 
-#> Attaching package: 'dplyr'
-#> The following objects are masked from 'package:mia':
-#> 
-#>     full_join, inner_join, left_join, right_join
-#> The following objects are masked from 'package:Biostrings':
-#> 
-#>     collapse, intersect, setdiff, setequal, union
-#> The following object is masked from 'package:XVector':
-#> 
-#>     slice
-#> The following object is masked from 'package:Biobase':
-#> 
-#>     combine
-#> The following objects are masked from 'package:GenomicRanges':
-#> 
-#>     intersect, setdiff, union
-#> The following object is masked from 'package:GenomeInfoDb':
-#> 
-#>     intersect
-#> The following objects are masked from 'package:IRanges':
-#> 
-#>     collapse, desc, intersect, setdiff, slice, union
-#> The following objects are masked from 'package:S4Vectors':
-#> 
-#>     first, intersect, rename, setdiff, setequal, union
-#> The following objects are masked from 'package:BiocGenerics':
-#> 
-#>     combine, intersect, setdiff, union
-#> The following object is masked from 'package:matrixStats':
-#> 
-#>     count
-#> The following objects are masked from 'package:stats':
-#> 
-#>     filter, lag
-#> The following objects are masked from 'package:base':
-#> 
-#>     intersect, setdiff, setequal, union
 
 # List subjects with two time points
 selected.subjects <- names(which(table(tse$subject)==2))
 
 # Subjects counts per number of time points available in the data
 table(table(tse$subject)) %>% as.data.frame() %>%
-    rename(Timepoints=Var1, Subjects=Freq)
-#>   Timepoints Subjects
-#> 1          1      928
-#> 2          2       40
-#> 3          3       23
-#> 4          4        1
-#> 5          5       14
+ rename(Timepoints=Var1, Subjects=Freq)

Lets look at all trajectories having two time points in the data:

-
+
 # plot
 p + geom_path(aes(x=X1, y=X2, group=subject), 
               arrow=arrow(length = unit(0.1, "inches")),
@@ -461,1020 +428,12 @@ 
Serial data ordination and traj
                             subject %in% selected.subjects) %>% arrange(time))+
     labs(title = "All trajectories with two time points")+
     theme(plot.title = element_text(hjust = 0.5))

-

 
Filtering the two time point trajectories by divergence and
 displaying top 10%:

-
+
 library(miaTime)
 # calculating step wise divergence based on the microbial profiles
 tse <- getStepwiseDivergence(tse, group = "subject", time_field = "time")
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 # retrieving the top 10% divergent subjects having two time points
 top.selected.subjects <- subset(data.frame(reducedDim(tse), colData(tse)),
                             subject %in% selected.subjects) %>% 
@@ -1495,10 +454,9 @@ 
Serial data ordination and traj
     labs(title = "Top 10%  divergent trajectories from time point one to two")+
     scale_color_gradient2(low="white", high="red")+
     theme(plot.title = element_text(hjust = 0.5))

-

 
Plotting an example of the trajectory with the maximum total
 divergence:

-
+
 # Get subject with the maximum total divergence
 selected.subject <- data.frame(reducedDim(tse), colData(tse)) %>%
     group_by(subject) %>% 
@@ -1511,7 +469,6 @@ 
Serial data ordination and traj
               arrow=arrow(length = unit(0.1, "inches")))+
     labs(title = "Longest trajectory by divergence")+
     theme(plot.title = element_text(hjust = 0.5))

-

 
More examples and materials are available at Orchestrating Microbiome
 Analysis (Lahti, Shetty, and Ernst
 2021).

@@ -1519,7 +476,7 @@ 
Serial data ordination and traj
 

 
Session info
 

-
+
 sessionInfo()
 #> R version 4.3.1 (2023-06-16)
 #> Platform: x86_64-pc-linux-gnu (64-bit)
@@ -1545,90 +502,79 @@ 
Session info#> [8] base     
 #> 
 #> other attached packages:
-#>  [1] dplyr_1.1.2                    miaTime_0.1.21                
-#>  [3] scater_1.29.4                  scuttle_1.11.2                
-#>  [5] patchwork_1.1.3                miaViz_1.9.2                  
-#>  [7] ggraph_2.1.0                   ggplot2_3.4.3                 
-#>  [9] mia_1.9.12                     MultiAssayExperiment_1.27.5   
-#> [11] TreeSummarizedExperiment_2.1.4 Biostrings_2.69.2             
-#> [13] XVector_0.41.1                 SingleCellExperiment_1.23.0   
-#> [15] SummarizedExperiment_1.31.1    Biobase_2.61.0                
-#> [17] GenomicRanges_1.53.1           GenomeInfoDb_1.37.3           
-#> [19] IRanges_2.35.2                 S4Vectors_0.39.1              
-#> [21] BiocGenerics_0.47.0            MatrixGenerics_1.13.1         
-#> [23] matrixStats_1.0.0              BiocStyle_2.29.1              
+#>  [1] miaTime_0.1.21                 scater_1.29.4                 
+#>  [3] scuttle_1.11.2                 patchwork_1.1.3               
+#>  [5] miaViz_1.9.3                   ggraph_2.1.0                  
+#>  [7] ggplot2_3.4.3                  mia_1.9.18                    
+#>  [9] MultiAssayExperiment_1.27.5    TreeSummarizedExperiment_2.1.4
+#> [11] Biostrings_2.69.2              XVector_0.41.1                
+#> [13] SingleCellExperiment_1.23.0    SummarizedExperiment_1.31.1   
+#> [15] Biobase_2.61.0                 GenomicRanges_1.53.1          
+#> [17] GenomeInfoDb_1.37.5            IRanges_2.35.2                
+#> [19] S4Vectors_0.39.2               BiocGenerics_0.47.0           
+#> [21] MatrixGenerics_1.13.1          matrixStats_1.0.0             
+#> [23] BiocStyle_2.29.2              
 #> 
 #> loaded via a namespace (and not attached):
-#>   [1] splines_4.3.1               later_1.3.1                
-#>   [3] bitops_1.0-7                ggplotify_0.1.2            
-#>   [5] tibble_3.2.1                polyclip_1.10-4            
-#>   [7] DirichletMultinomial_1.43.0 lifecycle_1.0.3            
-#>   [9] rprojroot_2.0.3             processx_3.8.2             
-#>  [11] lattice_0.21-8              MASS_7.3-60                
-#>  [13] magrittr_2.0.3              sass_0.4.7                 
-#>  [15] rmarkdown_2.24              remotes_2.4.2.1            
-#>  [17] jquerylib_0.1.4             yaml_2.3.7                 
-#>  [19] httpuv_1.6.11               sessioninfo_1.2.2          
-#>  [21] pkgbuild_1.4.2              DBI_1.1.3                  
-#>  [23] RColorBrewer_1.1-3          abind_1.4-5                
-#>  [25] pkgload_1.3.2.1             zlibbioc_1.47.0            
-#>  [27] purrr_1.0.2                 RCurl_1.98-1.12            
-#>  [29] yulab.utils_0.0.8           tweenr_2.0.2               
-#>  [31] GenomeInfoDbData_1.2.10     ggrepel_0.9.3              
-#>  [33] irlba_2.3.5.1               tidytree_0.4.5             
-#>  [35] vegan_2.6-4                 pkgdown_2.0.7              
-#>  [37] permute_0.9-7               DelayedMatrixStats_1.23.4  
-#>  [39] codetools_0.2-19            DelayedArray_0.27.10       
-#>  [41] ggforce_0.4.1               tidyselect_1.2.0           
-#>  [43] aplot_0.2.0                 farver_2.1.1               
-#>  [45] ScaledMatrix_1.9.1          viridis_0.6.4              
-#>  [47] jsonlite_1.8.7              BiocNeighbors_1.19.0       
-#>  [49] decontam_1.21.0             ellipsis_0.3.2             
-#>  [51] tidygraph_1.2.3             systemfonts_1.0.4          
-#>  [53] tools_4.3.1                 ggnewscale_0.4.9           
-#>  [55] treeio_1.25.4               ragg_1.2.5                 
-#>  [57] Rcpp_1.0.11                 glue_1.6.2                 
-#>  [59] gridExtra_2.3               SparseArray_1.1.11         
-#>  [61] xfun_0.40                   mgcv_1.9-0                 
-#>  [63] usethis_2.2.2               withr_2.5.0                
-#>  [65] BiocManager_1.30.22         fastmap_1.1.1              
-#>  [67] bluster_1.11.4              fansi_1.0.4                
-#>  [69] callr_3.7.3                 digest_0.6.33              
-#>  [71] rsvd_1.0.5                  R6_2.5.1                   
-#>  [73] mime_0.12                   gridGraphics_0.5-1         
-#>  [75] textshaping_0.3.6           colorspace_2.1-0           
-#>  [77] RSQLite_2.3.1               utf8_1.2.3                 
-#>  [79] tidyr_1.3.0                 generics_0.1.3             
-#>  [81] DECIPHER_2.29.0             prettyunits_1.1.1          
-#>  [83] graphlayouts_1.0.0          htmlwidgets_1.6.2          
-#>  [85] S4Arrays_1.1.5              pkgconfig_2.0.3            
-#>  [87] gtable_0.3.4                blob_1.2.4                 
-#>  [89] htmltools_0.5.6             profvis_0.3.8              
-#>  [91] bookdown_0.35               scales_1.2.1               
-#>  [93] ggfun_0.1.2                 knitr_1.43                 
-#>  [95] reshape2_1.4.4              nlme_3.1-163               
-#>  [97] cachem_1.0.8                stringr_1.5.0              
-#>  [99] parallel_4.3.1              miniUI_0.1.1.1             
-#> [101] vipor_0.4.5                 desc_1.4.2                 
-#> [103] pillar_1.9.0                grid_4.3.1                 
-#> [105] vctrs_0.6.3                 urlchecker_1.0.1           
-#> [107] promises_1.2.1              BiocSingular_1.17.1        
-#> [109] beachmat_2.17.15            xtable_1.8-4               
-#> [111] cluster_2.1.4               beeswarm_0.4.0             
-#> [113] evaluate_0.21               cli_3.6.1                  
-#> [115] compiler_4.3.1              rlang_1.1.1                
-#> [117] crayon_1.5.2                labeling_0.4.3             
-#> [119] ps_1.7.5                    plyr_1.8.8                 
-#> [121] fs_1.6.3                    ggbeeswarm_0.7.2           
-#> [123] stringi_1.7.12              viridisLite_0.4.2          
-#> [125] BiocParallel_1.35.4         munsell_0.5.0              
-#> [127] lazyeval_0.2.2              devtools_2.4.5             
-#> [129] Matrix_1.6-1                sparseMatrixStats_1.13.4   
-#> [131] bit64_4.0.5                 shiny_1.7.5                
-#> [133] highr_0.10                  igraph_1.5.1               
-#> [135] memoise_2.0.1               bslib_0.5.1                
-#> [137] ggtree_3.9.1                bit_4.0.5                  
-#> [139] ape_5.7-1

+#>   [1] RColorBrewer_1.1-3          jsonlite_1.8.7             
+#>   [3] magrittr_2.0.3              ggbeeswarm_0.7.2           
+#>   [5] farver_2.1.1                rmarkdown_2.25             
+#>   [7] fs_1.6.3                    zlibbioc_1.47.0            
+#>   [9] ragg_1.2.5                  vctrs_0.6.3                
+#>  [11] memoise_2.0.1               DelayedMatrixStats_1.23.4  
+#>  [13] RCurl_1.98-1.12             ggtree_3.9.1               
+#>  [15] htmltools_0.5.6             S4Arrays_1.1.6             
+#>  [17] BiocNeighbors_1.19.0        gridGraphics_0.5-1         
+#>  [19] SparseArray_1.1.12          sass_0.4.7                 
+#>  [21] bslib_0.5.1                 desc_1.4.2                 
+#>  [23] plyr_1.8.9                  DECIPHER_2.29.2            
+#>  [25] cachem_1.0.8                igraph_1.5.1               
+#>  [27] lifecycle_1.0.3             pkgconfig_2.0.3            
+#>  [29] rsvd_1.0.5                  Matrix_1.6-1.1             
+#>  [31] R6_2.5.1                    fastmap_1.1.1              
+#>  [33] GenomeInfoDbData_1.2.10     aplot_0.2.1                
+#>  [35] digest_0.6.33               ggnewscale_0.4.9           
+#>  [37] colorspace_2.1-0            rprojroot_2.0.3            
+#>  [39] irlba_2.3.5.1               textshaping_0.3.6          
+#>  [41] RSQLite_2.3.1               vegan_2.6-4                
+#>  [43] beachmat_2.17.16            labeling_0.4.3             
+#>  [45] fansi_1.0.4                 polyclip_1.10-6            
+#>  [47] abind_1.4-5                 mgcv_1.9-0                 
+#>  [49] compiler_4.3.1              bit64_4.0.5                
+#>  [51] withr_2.5.1                 BiocParallel_1.35.4        
+#>  [53] viridis_0.6.4               DBI_1.1.3                  
+#>  [55] ggforce_0.4.1               MASS_7.3-60                
+#>  [57] DelayedArray_0.27.10        bluster_1.11.4             
+#>  [59] permute_0.9-7               tools_4.3.1                
+#>  [61] vipor_0.4.5                 beeswarm_0.4.0             
+#>  [63] ape_5.7-1                   glue_1.6.2                 
+#>  [65] nlme_3.1-163                grid_4.3.1                 
+#>  [67] cluster_2.1.4               reshape2_1.4.4             
+#>  [69] generics_0.1.3              gtable_0.3.4               
+#>  [71] tidyr_1.3.0                 BiocSingular_1.17.1        
+#>  [73] tidygraph_1.2.3             ScaledMatrix_1.9.1         
+#>  [75] utf8_1.2.3                  ggrepel_0.9.3              
+#>  [77] pillar_1.9.0                stringr_1.5.0              
+#>  [79] yulab.utils_0.1.0           splines_4.3.1              
+#>  [81] dplyr_1.1.3                 tweenr_2.0.2               
+#>  [83] treeio_1.25.4               lattice_0.21-8             
+#>  [85] bit_4.0.5                   tidyselect_1.2.0           
+#>  [87] DirichletMultinomial_1.43.0 knitr_1.44                 
+#>  [89] gridExtra_2.3               bookdown_0.35              
+#>  [91] xfun_0.40                   graphlayouts_1.0.1         
+#>  [93] stringi_1.7.12              ggfun_0.1.3                
+#>  [95] lazyeval_0.2.2              yaml_2.3.7                 
+#>  [97] evaluate_0.22               codetools_0.2-19           
+#>  [99] tibble_3.2.1                BiocManager_1.30.22        
+#> [101] ggplotify_0.1.2             cli_3.6.1                  
+#> [103] systemfonts_1.0.4           munsell_0.5.0              
+#> [105] jquerylib_0.1.4             Rcpp_1.0.11                
+#> [107] parallel_4.3.1              pkgdown_2.0.7              
+#> [109] blob_1.2.4                  sparseMatrixStats_1.13.4   
+#> [111] bitops_1.0-7                decontam_1.21.0            
+#> [113] viridisLite_0.4.2           tidytree_0.4.5             
+#> [115] scales_1.2.1                purrr_1.0.2                
+#> [117] crayon_1.5.2                rlang_1.1.1

 

 

 
References
diff --git a/articles/miaViz_files/figure-html/MDS-1.png b/articles/miaViz_files/figure-html/MDS-1.png
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diff --git a/authors.html b/authors.html
index 59bfed0c..a09e95ae 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       
       
         miaViz
-        1.9.2
+        1.9.3
       
     

 
@@ -58,6 +58,10 @@ 
Authors

           
Basil Courbayre. Contributor. 
           

         
+        
  • 
+          
    Giulio Benedetti. Contributor. 
+          
    
+        
    • 
       
    
     
    
     
    
@@ -69,13 +73,13 @@ 
    Citation
    
 
     
    Borman T, Ernst F, Lahti L (2023).
 miaViz: Microbiome Analysis Plotting and Visualization.
-R package version 1.9.2. 
+R package version 1.9.3. 
 
    
     
    @Manual{,
   title = {miaViz: Microbiome Analysis Plotting and Visualization},
   author = {Tuomas Borman and Felix G.M. Ernst and Leo Lahti},
   year = {2023},
-  note = {R package version 1.9.2},
+  note = {R package version 1.9.3},
 }
    
 
   
    
diff --git a/index.html b/index.html
index 8d8d48b6..6bc0310a 100644
--- a/index.html
+++ b/index.html
@@ -36,7 +36,7 @@
       
       
         miaViz
-        1.9.2
+        1.9.3
       
     
    
 
diff --git a/pkgdown.yml b/pkgdown.yml
index 25dcc606..6958a0c0 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   miaViz: miaViz.html
-last_built: 2023-08-30T13:32Z
+last_built: 2023-10-02T15:32Z
 
diff --git a/reference/Rplot008.png b/reference/Rplot008.png
index e07c8bb8..6d6b3b42 100644
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diff --git a/reference/index.html b/reference/index.html
index dc893eaa..6f9c0243 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
       
       
         miaViz
-        1.9.2
+        1.9.3
       
     
    
 
@@ -64,6 +64,10 @@ 
    All functions plotAbundanceDensity() 
    
         
         
    Plot abundance density
    
+      
+          
    plotCCA() plotRDA() 
    
+        
+        
    Plot RDA or CCA object
    
       
           
    plotColTile() plotRowTile() 
    
         
diff --git a/reference/mia-datasets.html b/reference/mia-datasets.html
index 5c7bfe20..688bb058 100644
--- a/reference/mia-datasets.html
+++ b/reference/mia-datasets.html
@@ -18,7 +18,7 @@
       
       
         miaViz
-        1.9.2
+        1.9.3
    diff --git a/reference/mia-plot-args.html b/reference/mia-plot-args.html index 8bfbb4d7..287702ab 100644 --- a/reference/mia-plot-args.html +++ b/reference/mia-plot-args.html @@ -18,7 +18,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/reference/miaViz-package.html b/reference/miaViz-package.html index e44d3009..e95b16c0 100644 --- a/reference/miaViz-package.html +++ b/reference/miaViz-package.html @@ -19,7 +19,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/reference/plotAbundance.html b/reference/plotAbundance.html index 62162b28..b8ea18c5 100644 --- a/reference/plotAbundance.html +++ b/reference/plotAbundance.html @@ -20,7 +20,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/reference/plotAbundanceDensity-1.png b/reference/plotAbundanceDensity-1.png index ac8bc9bb..8dbac73a 100644 Binary files a/reference/plotAbundanceDensity-1.png and b/reference/plotAbundanceDensity-1.png differ diff --git a/reference/plotAbundanceDensity-2.png b/reference/plotAbundanceDensity-2.png index 69a45223..e2123228 100644 Binary files a/reference/plotAbundanceDensity-2.png and b/reference/plotAbundanceDensity-2.png differ diff --git a/reference/plotAbundanceDensity-6.png b/reference/plotAbundanceDensity-6.png index 8df46390..5d4019ed 100644 Binary files a/reference/plotAbundanceDensity-6.png and b/reference/plotAbundanceDensity-6.png differ diff --git a/reference/plotAbundanceDensity-7.png b/reference/plotAbundanceDensity-7.png index 84526cf2..004c41de 100644 Binary files a/reference/plotAbundanceDensity-7.png and b/reference/plotAbundanceDensity-7.png differ diff --git a/reference/plotAbundanceDensity.html b/reference/plotAbundanceDensity.html index 70890023..82310311 100644 --- a/reference/plotAbundanceDensity.html +++ b/reference/plotAbundanceDensity.html @@ -17,7 +17,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/reference/plotCCA-1.png b/reference/plotCCA-1.png new file mode 100644 index 00000000..e5fb495e Binary files /dev/null and b/reference/plotCCA-1.png differ diff --git a/reference/plotCCA-2.png b/reference/plotCCA-2.png new file mode 100644 index 00000000..32b02323 Binary files /dev/null and b/reference/plotCCA-2.png differ diff --git a/reference/plotCCA-3.png b/reference/plotCCA-3.png new file mode 100644 index 00000000..e9053257 Binary files /dev/null and b/reference/plotCCA-3.png differ diff --git a/reference/plotCCA-4.png b/reference/plotCCA-4.png new file mode 100644 index 00000000..1c05ea29 Binary files /dev/null and b/reference/plotCCA-4.png differ diff --git a/reference/plotCCA-5.png b/reference/plotCCA-5.png new file mode 100644 index 00000000..b31a7873 Binary files /dev/null and b/reference/plotCCA-5.png differ diff --git a/reference/plotCCA-6.png b/reference/plotCCA-6.png new file mode 100644 index 00000000..3464c38c Binary files /dev/null and b/reference/plotCCA-6.png differ diff --git a/reference/plotCCA.html b/reference/plotCCA.html new file mode 100644 index 00000000..78c260b8 --- /dev/null +++ b/reference/plotCCA.html @@ -0,0 +1,335 @@ + +Plot RDA or CCA object — plotCCA • miaViz + + +
    +
    + + + +
    +
    +
    +

    Plot RDA or CCA object

    + + +
    + +
    +

    plotRDA and plotCCA create an RDA/CCA plot starting from the +output of CCA and RDA functions, two common methods +for supervised ordination of microbiome data.

    +
    + +
    + 
    plotCCA(object, ...)
+
+# S4 method for SingleCellExperiment
+plotCCA(object, dimred, ...)
+
+# S4 method for matrix
+plotCCA(object, ...)
+
+plotRDA(object, ...)
+
+# S4 method for SingleCellExperiment
+plotRDA(
+  object,
+  dimred,
+  add.ellipse = TRUE,
+  ellipse.alpha = 0.2,
+  ellipse.linewidth = 0.1,
+  ellipse.linetype = 1,
+  vec.size = 0.5,
+  vec.color = vec.colour,
+  vec.colour = "black",
+  vec.linetype = 1,
+  arrow.size = 0.25,
+  label.color = label.colour,
+  label.colour = "black",
+  label.size = 4,
+  vec.text = TRUE,
+  repel.labels = TRUE,
+  sep.group = "‒",
+  repl.underscore = " ",
+  add.significance = TRUE,
+  add.expl.var = TRUE,
+  add.vectors = TRUE,
+  parse.labels = TRUE,
+  ...
+)
+
+# S4 method for matrix
+plotRDA(object, ...)
    +
    + +
    +

    Arguments

    +
    object
    +

    a +TreeSummarizedExperiment +or a matrix of weights. The latter is returned as output from calculateRDA.

    + + +
    ...
    +

    additional parameters for plotting, inherited from +plotReducedDim, +geom_label and +geom_label_repel.

    + + +
    dimred
    +

    A string or integer scalar indicating the reduced dimension to +plot. This is the output of runRDA and resides in +reducedDim(tse, dimred).

    + + +
    add.ellipse
    +

    One of c(TRUE, FALSE, "fill", "colour", "color"), +indicating whether ellipses should be present, absent, filled or colored. +(default: ellipse.fill = TRUE)

    + + +
    ellipse.alpha
    +

    Number between 0 and 1 to adjust the opacity of ellipses. +(default: ellipse.alpha = 0.2)

    + + +
    ellipse.linewidth
    +

    Number specifying the size of ellipses. +(default: ellipse.linewidth = 0.1)

    + + +
    ellipse.linetype
    +

    Discrete number specifying the style of ellipses. +(default: ellipse.linetype = 1)

    + + +
    vec.size
    +

    Number specifying the size of vectors. +(default: vec.size = 0.5)

    + + +
    vec.color
    +

    Alias for vec.colour.

    + + +
    vec.colour
    +

    String specifying the colour of vectors. +(default: vec.color = "black")

    + + +
    vec.linetype
    +

    Discrete number specifying the style of vector lines. +(default: vec.linetype = 1)

    + + +
    arrow.size
    +

    Number specifying the size of arrows. +(defaults: arrow.size = 0.25)

    + + +
    label.color
    +

    Alias for label.colour.

    + + +
    label.colour
    +

    String specifying the colour of text and labels. +(default: label.color = "black")

    + + +
    label.size
    +

    Number specifying the size of text and labels. +(default: label.size = 4)

    + + +
    vec.text
    +

    TRUE or FALSE, should text instead of labels be used to label vectors. +(default: vec.text = TRUE)

    + + +
    repel.labels
    +

    TRUE or FALSE, should labels be repelled. +(default: repel.labels = TRUE)

    + + +
    sep.group
    +

    String specifying the separator used in the labels. +(default: sep.group = "\U2012")

    + + +
    repl.underscore
    +

    String used to replace underscores in the labels. +(default: repl.underscore = " ")

    + + +
    add.significance
    +

    TRUE or FALSE, should explained variance and p-value +appear in the labels. (default: add.significance = TRUE)

    + + +
    add.expl.var
    +

    TRUE or FALSE, should explained variance appear on the +coordinate axes. (default: add.expl.var = TRUE)

    + + +
    add.vectors
    +

    TRUE or FALSE, should vectors appear in the plot. +(default: add.vectors = TRUE)

    + + +
    parse.labels
    +

    TRUE or FALSE, should labels be parsed. +(default: parse.labels = TRUE)

    + +
    +
    +

    Value

    + + +

    A ggplot2 object

    +
    +
    +

    Details

    +

    plotRDA and plotCCA create an RDA/CCA plot starting from the +output of CCA and RDA functions, two common methods +for supervised ordination of microbiome data. Either a +TreeSummarizedExperiment +or a matrix object is supported as input. When the input is a +TreeSummarizedExperiment, this should contain the output of runRDA +in the reducedDim slot and the argument dimred needs to be defined. +When the input is a matrix, this should be returned as output from +calculateRDA. However, the first method is recommended because it provides +the option to adjust aesthetics to the colData variables through the +arguments inherited from plotReducedDim.

    +
    + +
    +

    Examples

    + 
    # Load dataset
+library(miaViz)
+data("enterotype", package = "mia")
+tse <- enterotype
+ 
+# Run RDA and store results into TreeSE
+tse <- runRDA(tse,
+              formula = assay ~ ClinicalStatus + Gender + Age,
+              FUN = vegan::vegdist,
+              distance = "bray",
+              na.action = na.exclude)
+               
+# Create RDA plot coloured by variable
+plotRDA(tse, "RDA",
+        colour_by = "ClinicalStatus")
+#> Warning: Removed 243 rows containing non-finite values (`stat_ellipse()`).
+#> Too few points to calculate an ellipse
+#> Too few points to calculate an ellipse
+#> Warning: Removed 243 rows containing missing values (`geom_point()`).
+
+ 
+# Create RDA plot with empty ellipses
+plotRDA(tse, "RDA",
+        colour_by = "ClinicalStatus",
+        add.ellipse = "colour")
+#> Warning: Removed 243 rows containing non-finite values (`stat_ellipse()`).
+#> Too few points to calculate an ellipse
+#> Too few points to calculate an ellipse
+#> Warning: Removed 243 rows containing missing values (`geom_point()`).
+
+ 
+# Create RDA plot with text encased in labels
+plotRDA(tse, "RDA",
+        colour_by = "ClinicalStatus",
+        vec.text = FALSE)
+#> Warning: Removed 243 rows containing non-finite values (`stat_ellipse()`).
+#> Too few points to calculate an ellipse
+#> Too few points to calculate an ellipse
+#> Warning: Removed 243 rows containing missing values (`geom_point()`).
+
+ 
+# Create RDA plot without repelling text
+plotRDA(tse, "RDA",
+        colour_by = "ClinicalStatus",
+        repel.labels = FALSE)
+#> Warning: Removed 243 rows containing non-finite values (`stat_ellipse()`).
+#> Too few points to calculate an ellipse
+#> Too few points to calculate an ellipse
+#> Warning: Removed 243 rows containing missing values (`geom_point()`).
+
+ 
+# Create RDA plot without vectors
+plotRDA(tse, "RDA",
+        colour_by = "ClinicalStatus",
+        add.vectors = FALSE)
+#> Warning: 'add.vectors' is FALSE, so other arguments for vectors and labels will be disregarded.
+#> Warning: Removed 243 rows containing non-finite values (`stat_ellipse()`).
+#> Too few points to calculate an ellipse
+#> Too few points to calculate an ellipse
+#> Warning: Removed 243 rows containing missing values (`geom_point()`).
+
+ 
+# Calculate RDA as a separate object
+rda_mat <- calculateRDA(tse,
+                        formula = assay ~ ClinicalStatus + Gender + Age,
+                        FUN = vegan::vegdist,
+                        distance = "bray",
+                        na.action = na.exclude)
+ 
+# Create RDA plot from RDA matrix
+plotRDA(rda_mat)
+
+
    +
    +
    + +
    + + +
    +

    Developed by Tuomas Borman, Felix G.M. Ernst, Leo Lahti.

    +
    + +
    +

    Site built with pkgdown 2.0.7.

    +
    + +
    + + + + + + + + diff --git a/reference/plotColTile.html b/reference/plotColTile.html index dc2b4540..decbaae7 100644 --- a/reference/plotColTile.html +++ b/reference/plotColTile.html @@ -19,7 +19,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/reference/plotDMN-1.png b/reference/plotDMN-1.png index 9d194570..e1776dd6 100644 Binary files a/reference/plotDMN-1.png and b/reference/plotDMN-1.png differ diff --git a/reference/plotDMN.html b/reference/plotDMN.html index 01cca596..b0acc171 100644 --- a/reference/plotDMN.html +++ b/reference/plotDMN.html @@ -17,7 +17,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/reference/plotGraph-1.png b/reference/plotGraph-1.png index ee7f6180..f5552e8e 100644 Binary files a/reference/plotGraph-1.png and b/reference/plotGraph-1.png differ diff --git a/reference/plotGraph-6.png b/reference/plotGraph-6.png index 39143a3b..c59adfca 100644 Binary files a/reference/plotGraph-6.png and b/reference/plotGraph-6.png differ diff --git a/reference/plotGraph-7.png b/reference/plotGraph-7.png index edd68fe8..11c06dd3 100644 Binary files a/reference/plotGraph-7.png and b/reference/plotGraph-7.png differ diff --git a/reference/plotGraph-8.png b/reference/plotGraph-8.png index 87fee6e5..1bf0c4d3 100644 Binary files a/reference/plotGraph-8.png and b/reference/plotGraph-8.png differ diff --git a/reference/plotGraph.html b/reference/plotGraph.html index 159c95fe..63f96293 100644 --- a/reference/plotGraph.html +++ b/reference/plotGraph.html @@ -19,7 +19,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/reference/plotPrevalence.html b/reference/plotPrevalence.html index 9916b135..83ef3a65 100644 --- a/reference/plotPrevalence.html +++ b/reference/plotPrevalence.html @@ -18,7 +18,7 @@ miaViz - 1.9.2 + 1.9.3 @@ -227,7 +227,7 @@

    Examples

    # plotting N of prevalence exceeding taxa on the Phylum level plotPrevalence(GlobalPatterns, rank = "Phylum") -plotPrevalence(GlobalPatterns, rank = "Phylum") + scale_x_log10() +plotPrevalence(GlobalPatterns, rank = "Phylum") + scale_x_log10() # plotting prevalence per taxa for different detection thresholds as heatmap @@ -244,14 +244,14 @@

    Examples

    # information plotPrevalentAbundance(GlobalPatterns, rank = "Family", colour_by = "Phylum") + - scale_x_log10() + scale_x_log10() # When using function plotPrevalentAbundace, it is possible to create facets # with 'facet_by'. plotPrevalentAbundance(GlobalPatterns, rank = "Family", colour_by = "Phylum", facet_by = "Kingdom") + - scale_x_log10() + scale_x_log10() diff --git a/reference/plotSeries.html b/reference/plotSeries.html index 19208f93..76ce661b 100644 --- a/reference/plotSeries.html +++ b/reference/plotSeries.html @@ -17,7 +17,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/reference/plotTree.html b/reference/plotTree.html index be214914..70cb4cc1 100644 --- a/reference/plotTree.html +++ b/reference/plotTree.html @@ -20,7 +20,7 @@ miaViz - 1.9.2 + 1.9.3 diff --git a/reference/treeData.html b/reference/treeData.html index 3923e0cd..c9de8b0f 100644 --- a/reference/treeData.html +++ b/reference/treeData.html @@ -19,7 +19,7 @@ miaViz - 1.9.2 + 1.9.3 @@ -183,18 +183,18 @@

    Examples

    #> #> # The associated data tibble abstraction: 38,431 × 4 #> # The 'node', 'label' and 'isTip' are from the phylo tree. -#> node label isTip test -#> <int> <chr> <lgl> <dbl> -#> 1 1 549322 TRUE 0.0822 -#> 2 2 522457 TRUE -1.60 -#> 3 3 951 TRUE 0.722 -#> 4 4 244423 TRUE -0.440 -#> 5 5 586076 TRUE -1.07 -#> 6 6 246140 TRUE -1.52 -#> 7 7 143239 TRUE 1.60 -#> 8 8 244960 TRUE 0.668 -#> 9 9 255340 TRUE -0.0879 -#> 10 10 144887 TRUE -0.0426 +#> node label isTip test +#> <int> <chr> <lgl> <dbl> +#> 1 1 549322 TRUE -0.871 +#> 2 2 522457 TRUE -1.17 +#> 3 3 951 TRUE 1.90 +#> 4 4 244423 TRUE -0.942 +#> 5 5 586076 TRUE -0.177 +#> 6 6 246140 TRUE -1.51 +#> 7 7 143239 TRUE -0.679 +#> 8 8 244960 TRUE 0.657 +#> 9 9 255340 TRUE -1.67 +#> 10 10 144887 TRUE -1.63 #> # ℹ 38,421 more rows diff --git a/sitemap.xml b/sitemap.xml index 0a295d43..95202576 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -36,6 +36,9 @@ /reference/plotAbundanceDensity.html + + /reference/plotCCA.html + /reference/plotColTile.html