diff --git a/R/SCP-plot.R b/R/SCP-plot.R
index e3d82e4d..b47b7007 100644
--- a/R/SCP-plot.R
+++ b/R/SCP-plot.R
@@ -2763,12 +2763,13 @@ FeatureDimPlot <- function(srt, features, reduction = NULL, dims = c(1, 2), spli
#' Plotting cell points on a reduced 3D space and coloring according to the groups of the cells.
#'
#' @inheritParams CellDimPlot
+#' @param dims Dimensions to plot, must be a three-length numeric vector specifying x-, y- and z-dimensions
#' @param axis_labs A character vector of length 3 indicating the labels for the axes.
#' @param span A numeric value specifying the span of the loess smoother for lineages line.
#' @param shape.highlight Shape of the cell to highlight. See \href{https://plotly.com/r/reference/scattergl/#scattergl-marker-symbol}{scattergl-marker-symbol}
#' @param width Width in pixels, defaults to automatic sizing.
#' @param height Height in pixels, defaults to automatic sizing.
-#' @param save The name of the file to save the plot to. Must end in .html.
+#' @param save The name of the file to save the plot to. Must end in ".html".
#' @seealso \code{\link{CellDimPlot}} \code{\link{FeatureDimPlot3D}}
#'
#' @examples
@@ -2778,6 +2779,7 @@ FeatureDimPlot <- function(srt, features, reduction = NULL, dims = c(1, 2), spli
#'
#' pancreas_sub <- RunSlingshot(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUMAP3D")
#' CellDimPlot3D(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUMAP3D", lineages = "Lineage1")
+#'
#' @importFrom Seurat Reductions Embeddings Key
#' @importFrom utils askYesNo
#' @importFrom plotly plot_ly add_trace layout as_widget
@@ -2857,9 +2859,6 @@ CellDimPlot3D <- function(srt, group.by, reduction = NULL, dims = c(1, 2, 3), ax
dat_lineages <- srt@meta.data[, unique(lineages), drop = FALSE]
dat_use <- cbind(dat_use, dat_lineages[row.names(dat_use), , drop = FALSE])
}
- if (!is.factor(dat_use[[group.by]])) {
- dat_use[[group.by]] <- factor(dat_use[[group.by]], levels = unique(dat_use[[group.by]]))
- }
dat_use[["group.by"]] <- dat_use[[group.by]]
if (any(is.na(dat_use[[group.by]]))) {
n <- as.character(dat_use[[group.by]])
diff --git a/R/SCP-workflow.R b/R/SCP-workflow.R
index c90761f9..38ed6087 100644
--- a/R/SCP-workflow.R
+++ b/R/SCP-workflow.R
@@ -838,7 +838,8 @@ RunDimReduction <- function(srt, prefix = "", features = NULL, assay = NULL, slo
srt@misc[["Default_reduction"]] <- paste0(prefix, linear_reduction)
return(srt)
} else {
- message("assay.used is ", srt[[linear_reduction]]@assay.used, ", which is not the same as the ", assay, " specified. Recalculate the linear reduction")
+ message("assay.used is ", srt[[linear_reduction]]@assay.used, ", which is not the same as the ", assay, " specified. Recalculate the linear reduction(pca)")
+ linear_reduction <- "pca"
}
}
}
@@ -933,7 +934,8 @@ RunDimReduction <- function(srt, prefix = "", features = NULL, assay = NULL, slo
srt@misc[["Default_reduction"]] <- paste0(prefix, nonlinear_reduction)
return(srt)
} else {
- message("assay.used is ", srt[[nonlinear_reduction]]@assay.used, ", which is not the same as the ", assay, " specified. Recalculate the linear reduction")
+ message("assay.used is ", srt[[nonlinear_reduction]]@assay.used, ", which is not the same as the ", assay, " specified. Recalculate the nonlinear reduction(umap)")
+ nonlinear_reduction <- "umap"
}
}
}
@@ -1031,7 +1033,7 @@ DefaultReduction <- function(srt, pattern = NULL, min_dim = 2, max_distance = 0.
if (length(srt@reductions) == 0) {
stop("Unable to find any reductions.")
}
- pattern_default <- c("umap", "tsne", "dm", "phate", "pacmap", "trimap", "largevis", "pca", "svd", "ica", "nmf", "mds", "glmpca")
+ pattern_default <- c("umap", "tsne", "dm", "phate", "pacmap", "trimap", "largevis", "fr", "pca", "svd", "ica", "nmf", "mds", "glmpca")
pattern_dim <- c("2D", "3D")
reduc_all <- names(srt@reductions)
reduc_all <- reduc_all[unlist(lapply(reduc_all, function(x) {
@@ -3204,11 +3206,11 @@ Conos_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLis
}
cat(paste0("[", Sys.time(), "]", " Perform linear dimension reduction (", linear_reduction, ") on the data ", i, " ...\n"))
srt <- RunDimReduction(
- srt = srt, prefix = "", features = HVF, assay = DefaultAssay(srt),
+ srt = srt, prefix = "Conos", features = HVF, assay = DefaultAssay(srt),
linear_reduction = linear_reduction, linear_reduction_dims = linear_reduction_dims, linear_reduction_params = linear_reduction_params, force_linear_reduction = force_linear_reduction,
verbose = FALSE, seed = seed
)
- srt[["pca"]] <- srt[[linear_reduction]]
+ srt[["pca"]] <- srt[[paste0("Conos", linear_reduction)]]
srtList[[i]] <- srt
}
if (is.null(names(srtList))) {
@@ -3216,13 +3218,13 @@ Conos_integrate <- function(srtMerge = NULL, batch = NULL, append = TRUE, srtLis
}
if (is.null(linear_reduction_dims_use)) {
- maxdims <- max(unlist(sapply(srtList, function(srt) max(srt@reductions[[paste0("", linear_reduction)]]@misc[["dims_estimate"]]))))
+ maxdims <- max(unlist(sapply(srtList, function(srt) max(srt@reductions[[paste0("Conos", linear_reduction)]]@misc[["dims_estimate"]]))))
} else {
maxdims <- max(linear_reduction_dims_use)
}
cat(paste0("[", Sys.time(), "]", " Perform integration(Conos) on the data...\n"))
- message("Conos using ", linear_reduction, "(dims_max:", maxdims, ") as input")
+ message("Conos integration using Reduction(", linear_reduction, ", dims_max:", maxdims, ") as input")
srtList_con <- conos::Conos$new(srtList, n.cores = num_threads)
params <- list(
ncomps = maxdims,
@@ -3739,14 +3741,18 @@ Standard_SCP <- function(srt, prefix = "Standard", assay = NULL,
#' for (method in integration_methods) {
#' panc8_sub <- Integration_SCP(
#' srtMerge = panc8_sub, batch = "tech",
-#' integration_method = method, linear_reduction_dims_use = 1:50, nonlinear_reduction = "umap"
+#' integration_method = method,
+#' linear_reduction_dims_use = 1:50,
+#' nonlinear_reduction = "umap"
#' )
#' print(CellDimPlot(panc8_sub, group.by = c("tech", "celltype"), reduction = paste0(method, "UMAP2D"), theme_use = "theme_blank"))
#' }
#'
#' nonlinear_reductions <- c("umap", "tsne", "dm", "phate", "pacmap", "trimap", "largevis", "fr")
#' panc8_sub <- Integration_SCP(
-#' srtMerge = panc8_sub, batch = "tech", integration_method = "Seurat",
+#' srtMerge = panc8_sub, batch = "tech",
+#' integration_method = "Seurat",
+#' linear_reduction_dims_use = 1:50,
#' nonlinear_reduction = nonlinear_reductions
#' )
#' for (nr in nonlinear_reductions) {
diff --git a/R/Seurat-function.R b/R/Seurat-function.R
index 0b03fd57..4ea2a9de 100644
--- a/R/Seurat-function.R
+++ b/R/Seurat-function.R
@@ -117,7 +117,7 @@ RunNMF.default <- function(object, assay = NULL, slot = "data", nbes = 50,
}
nbes <- min(nbes, nrow(x = object) - 1)
if (nmf.method == "RcppML") {
- check_R("zdebruine/RcppML@0.5.6")
+ check_R("zdebruine/RcppML")
options("RcppML.verbose" = FALSE)
options("RcppML.threads" = 0)
nmf.results <- RcppML::nmf(
@@ -1602,7 +1602,7 @@ RunLargeVis.Seurat <- function(object, reduction = "pca", dims = NULL, features
search_k = search_k, n_threads = n_threads, n_sgd_threads = n_sgd_threads, grain_size = grain_size,
kernel = kernel, pca = pca, pca_center = pca_center, pcg_rand = pcg_rand, fast_sgd = fast_sgd,
batch = batch, opt_args = opt_args, epoch_callback = epoch_callback, pca_method = pca_method,
- reduction.key = reduction.key, verbose = verbose, seed.use = seed.use, ...
+ reduction.key = reduction.key, verbose = verbose, seed.use = seed.use
)
object <- LogSeuratCommand(object = object)
return(object)
diff --git a/R/utils.R b/R/utils.R
index e51f8408..bf559893 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -9,7 +9,6 @@
#' If a conda environment with the specified name already exists and \code{force} is set to \code{FALSE}, the function will use the existing environment. If \code{force} set to \code{TRUE}, the existing environment will be recreated. Note that recreating the environment will remove any existing data in the environment.
#' The function also checks if the package versions in the environment meet the requirements specified by the \code{version} parameter. The default is \code{3.8-1}.
#'
-#'
#' @export
PrepareEnv <- function(conda = "auto", miniconda_repo = "https://repo.anaconda.com/miniconda",
envname = NULL, version = "3.8-1", force = FALSE, ...) {
@@ -142,8 +141,8 @@ PrepareEnv <- function(conda = "auto", miniconda_repo = "https://repo.anaconda.c
#' Env_requirements("3.8-1")
#'
#' @export
-Env_requirements <- function(version = c("3.8-1", "3.8-2", "3.9-1", "3.10-1", "3.11-1")) {
- version <- match.arg(version)
+Env_requirements <- function(version = "3.8-1") {
+ version <- match.arg(version, choices = c("3.8-1", "3.8-2", "3.9-1", "3.10-1", "3.11-1"))
requirements <- switch(version,
"3.8-1" = list(
python = "3.8",
@@ -159,7 +158,10 @@ Env_requirements <- function(version = c("3.8-1", "3.8-2", "3.9-1", "3.10-1", "3
"scikit-learn" = "scikit-learn==1.1.2",
"scipy" = "scipy==1.10.1",
"scvelo" = "scvelo==0.2.5",
- "wot" = "wot==1.0.8.post2"
+ "wot" = "wot==1.0.8.post2",
+ "trimap" = "trimap==1.1.4",
+ "pacmap" = "pacmap==0.7.0",
+ "phate" = "phate==1.0.11"
# "tables" = "git+https://github.com/PyTables/PyTables", # Fixed: PyTables install fails on macOS M1
)
),
@@ -168,7 +170,7 @@ Env_requirements <- function(version = c("3.8-1", "3.8-2", "3.9-1", "3.10-1", "3
packages = c(
"leidenalg" = "leidenalg==0.10.1",
"matplotlib" = "matplotlib==3.7.3",
- "numba" = "numba==0.58.0",
+ "numba" = "numba==0.58.1",
"numpy" = "numpy==1.24.4",
"palantir" = "palantir==1.3.0",
"pandas" = "pandas==1.5.3",
@@ -185,7 +187,7 @@ Env_requirements <- function(version = c("3.8-1", "3.8-2", "3.9-1", "3.10-1", "3
packages = c(
"leidenalg" = "leidenalg==0.10.1",
"matplotlib" = "matplotlib==3.8.0",
- "numba" = "numba==0.58.0",
+ "numba" = "numba==0.58.1",
"numpy" = "numpy==1.25.2",
"palantir" = "palantir==1.3.0",
"pandas" = "pandas==1.5.3",
@@ -202,7 +204,7 @@ Env_requirements <- function(version = c("3.8-1", "3.8-2", "3.9-1", "3.10-1", "3
packages = c(
"leidenalg" = "leidenalg==0.10.1",
"matplotlib" = "matplotlib==3.8.0",
- "numba" = "numba==0.58.0",
+ "numba" = "numba==0.58.1",
"numpy" = "numpy==1.25.2",
"palantir" = "palantir==1.3.0",
"pandas" = "pandas==1.5.3",
@@ -219,7 +221,7 @@ Env_requirements <- function(version = c("3.8-1", "3.8-2", "3.9-1", "3.10-1", "3
packages = c(
"leidenalg" = "leidenalg==0.10.1",
"matplotlib" = "matplotlib==3.8.0",
- "numba" = "numba==0.58.0",
+ "numba" = "numba==0.58.1",
"numpy" = "numpy==1.25.2",
"palantir" = "palantir==1.3.0",
"pandas" = "pandas==1.5.3",
@@ -519,8 +521,7 @@ check_Python <- function(packages, envname = NULL, conda = "auto", force = FALSE
#' Check and install R packages
#'
-#' @param packages Package to be installed. Package source can be CRAN, Bioconductor or Github, e.g. scmap, davidsjoberg/ggsankey.
-#' @param package_names The name of the package that corresponds to the \code{packages} parameter, used to check if the package is already installed.
+#' @param packages Package to be installed. Package source can be CRAN, Bioconductor or Github, e.g. scmap, quadbiolab/simspec.
#' By default, the package name is extracted according to the \code{packages} parameter.
#' @param install_methods Functions used to install R packages.
#' @param lib The location of the library directories where to install the packages.
@@ -528,31 +529,11 @@ check_Python <- function(packages, envname = NULL, conda = "auto", force = FALSE
#'
#' @importFrom utils packageVersion
#' @export
-check_R <- function(packages, package_names = NULL, install_methods = c("BiocManager::install", "install.packages", "devtools::install_github"), lib = .libPaths()[1], force = FALSE) {
- if (length(package_names) != 0 && length(package_names) != length(packages)) {
- stop("package_names must be NULL or a vector of the same length with packages")
- }
+check_R <- function(packages, install_methods = c("BiocManager::install", "install.packages", "devtools::install_github"), lib = .libPaths()[1], force = FALSE) {
status_list <- list()
- for (n in seq_along(packages)) {
- pkg <- packages[n]
- pkg_info <- pkg
- if (!grepl("/", pkg_info)) {
- pkg_info <- paste0("/", pkg_info)
- }
- if (!grepl("@", pkg_info)) {
- pkg_info <- paste0(pkg_info, "@")
- }
- git <- grep("/", sub(pattern = "(.*/)(.*)(@.*)", replacement = "\\1", x = pkg_info), value = TRUE)
- git <- gsub("/", "", git)
- pkg_name <- package_names[n] %||% sub(pattern = "(.*/)(.*)(@.*)", replacement = "\\2", x = pkg_info)
- version <- grep("@", sub(pattern = "(.*/)(.*)(@.*)", replacement = "\\3", x = pkg_info), value = TRUE)
- version <- gsub("@", "", version)
- if (version != "") {
- force_update <- isTRUE(packageVersion(pkg_name) < package_version(version)) || isTRUE(force)
- } else {
- force_update <- isTRUE(force)
- }
- if (!suppressPackageStartupMessages(requireNamespace(pkg_name, quietly = TRUE)) || isTRUE(force_update)) {
+ for (pkg in packages) {
+ pkg_name <- sub(pattern = "(.*)/(.*)", replacement = "\\2", x = pkg)
+ if (!suppressPackageStartupMessages(requireNamespace(pkg_name, quietly = TRUE)) || isTRUE(force)) {
message("Install package: \"", pkg_name, "\" ...")
status_list[[pkg]] <- FALSE
i <- 1
@@ -577,15 +558,7 @@ check_R <- function(packages, package_names = NULL, install_methods = c("BiocMan
}, error = function(e) {
status_list[[pkg]] <- FALSE
})
- if (version == "") {
- status_list[[pkg]] <- requireNamespace(pkg_name, quietly = TRUE)
- } else {
- if (requireNamespace(pkg_name, quietly = TRUE)) {
- status_list[[pkg]] <- packageVersion(pkg_name) >= package_version(version)
- } else {
- status_list[[pkg]] <- FALSE
- }
- }
+ status_list[[pkg]] <- requireNamespace(pkg_name, quietly = TRUE)
i <- i + 1
if (i > length(install_methods)) {
break
diff --git a/README.Rmd b/README.Rmd
index 6abe7b58..8221f50f 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -11,7 +11,7 @@ knitr::opts_chunk$set(
results = "hide",
message = FALSE,
warning = FALSE,
- fig.path = "README/README-",
+ fig.path = "man/figures/",
fig.height = 5,
fig.width = 10,
fig.align = "center",
@@ -57,7 +57,7 @@ if (!require("devtools", quietly = TRUE)) {
devtools::install_github("zhanghao-njmu/SCP")
```
-#### Create SCP python environment
+#### Create a python environment for SCP
To run functions such as `RunPAGA` or `RunSCVELO`, SCP requires [conda](https://docs.conda.io/en/latest/miniconda.html) to create a separate python environment. The default environment name is `"SCP_env"`. You can specify the environment name for SCP by setting `options(SCP_env_name="new_name")`
@@ -282,13 +282,13 @@ CellDimPlot(
CellDimPlot3D(srt = pancreas_sub, group.by = "SubCellType")
```
-
+
```{r FeatureDimPlot3D,eval=FALSE}
FeatureDimPlot3D(srt = pancreas_sub, features = c("Sox9", "Neurog3", "Fev", "Rbp4"))
```
-
+
### Integration pipeline
@@ -330,7 +330,7 @@ grob <- gtable_add_grob(grob, legend, t = 1, l = min(grob$layout[grepl(pattern =
panel_fix(grob, height = 2)
```
-
+
### Cell projection between single-cell datasets
@@ -540,10 +540,10 @@ if (interactive()) {
}
```
- 
+ 
### Other visualization examples
-[**CellDimPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellDimPlot.html) [**CellStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellStatPlot.html) [**FeatureStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/FeatureStatPlot.html) [**GroupHeatmap**](https://zhanghao-njmu.github.io/SCP/reference/GroupHeatmap.html)
+[**CellDimPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellDimPlot.html) [**CellStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellStatPlot.html) [**FeatureStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/FeatureStatPlot.html) [**GroupHeatmap**](https://zhanghao-njmu.github.io/SCP/reference/GroupHeatmap.html)
You can also find more examples in the documentation of the function: [Integration_SCP](https://zhanghao-njmu.github.io/SCP/reference/Integration_SCP.html), [RunKNNMap](https://zhanghao-njmu.github.io/SCP/reference/RunKNNMap.html), [RunMonocle3](https://zhanghao-njmu.github.io/SCP/reference/RunMonocle3.html), [RunPalantir](https://zhanghao-njmu.github.io/SCP/reference/RunPalantir.html), etc.
diff --git a/README.md b/README.md
index fe1e9dd2..e4b1694c 100644
--- a/README.md
+++ b/README.md
@@ -66,7 +66,7 @@ if (!require("devtools", quietly = TRUE)) {
devtools::install_github("zhanghao-njmu/SCP")
```
-#### Create SCP python environment
+#### Create a python environment for SCP
To run functions such as `RunPAGA` or `RunSCVELO`, SCP requires
[conda](https://docs.conda.io/en/latest/miniconda.html) to create a
@@ -253,7 +253,7 @@ CellDimPlot(
)
```
-
+
``` r
CellDimPlot(
@@ -262,7 +262,7 @@ CellDimPlot(
)
```
-
+
``` r
FeatureDimPlot(
@@ -271,7 +271,7 @@ FeatureDimPlot(
)
```
-
+
``` r
FeatureDimPlot(
@@ -281,7 +281,7 @@ FeatureDimPlot(
)
```
-
+
``` r
ht <- GroupHeatmap(
@@ -303,7 +303,7 @@ ht <- GroupHeatmap(
print(ht$plot)
```
-
+
### CellQC
@@ -312,13 +312,13 @@ pancreas_sub <- RunCellQC(srt = pancreas_sub)
CellDimPlot(srt = pancreas_sub, group.by = "CellQC", reduction = "UMAP")
```
-
+
``` r
CellStatPlot(srt = pancreas_sub, stat.by = "CellQC", group.by = "CellType", label = TRUE)
```
-
+
``` r
CellStatPlot(
@@ -331,7 +331,7 @@ CellStatPlot(
)
```
-
+
### Standard pipeline
@@ -343,19 +343,19 @@ CellDimPlot(
)
```
-
+
``` r
CellDimPlot3D(srt = pancreas_sub, group.by = "SubCellType")
```
-
+
``` r
FeatureDimPlot3D(srt = pancreas_sub, features = c("Sox9", "Neurog3", "Fev", "Rbp4"))
```
-
+
### Integration pipeline
@@ -371,11 +371,11 @@ CellDimPlot(
)
```
-
+
UMAP embeddings based on different integration methods in SCP:
-
+
### Cell projection between single-cell datasets
@@ -392,7 +392,7 @@ ProjectionPlot(
)
```
-
+
### Cell annotation using bulk RNA-seq datasets
@@ -402,7 +402,7 @@ pancreas_sub <- RunKNNPredict(srt_query = pancreas_sub, bulk_ref = ref_scMCA, fi
CellDimPlot(srt = pancreas_sub, group.by = "KNNPredict_classification", reduction = "UMAP", label = TRUE)
```
-
+
### Cell annotation using single-cell datasets
@@ -414,7 +414,7 @@ pancreas_sub <- RunKNNPredict(
CellDimPlot(srt = pancreas_sub, group.by = "KNNPredict_classification", reduction = "UMAP", label = TRUE)
```
-
+
``` r
@@ -426,7 +426,7 @@ pancreas_sub <- RunKNNPredict(
CellDimPlot(srt = pancreas_sub, group.by = "KNNPredict_classification", reduction = "UMAP", label = TRUE)
```
-
+
``` r
@@ -439,7 +439,7 @@ ht <- CellCorHeatmap(
print(ht$plot)
```
-
+
### PAGA analysis
@@ -451,7 +451,7 @@ pancreas_sub <- RunPAGA(
PAGAPlot(srt = pancreas_sub, reduction = "UMAP", label = TRUE, label_insitu = TRUE, label_repel = TRUE)
```
-
+
### Velocity analysis
@@ -470,13 +470,13 @@ pancreas_sub <- RunSCVELO(
VelocityPlot(srt = pancreas_sub, reduction = "UMAP", group_by = "SubCellType")
```
-
+
``` r
VelocityPlot(srt = pancreas_sub, reduction = "UMAP", plot_type = "stream")
```
-
+
### Differential expression analysis
@@ -485,7 +485,7 @@ pancreas_sub <- RunDEtest(srt = pancreas_sub, group_by = "CellType", fc.threshol
VolcanoPlot(srt = pancreas_sub, group_by = "CellType")
```
-
+
``` r
DEGs <- pancreas_sub@tools$DEtest_CellType$AllMarkers_wilcox
@@ -501,7 +501,7 @@ ht <- FeatureHeatmap(
print(ht$plot)
```
-
+
### Enrichment analysis(over-representation)
@@ -516,7 +516,7 @@ EnrichmentPlot(
)
```
-
+
``` r
EnrichmentPlot(
@@ -525,7 +525,7 @@ EnrichmentPlot(
)
```
-
+
``` r
EnrichmentPlot(
@@ -534,7 +534,7 @@ EnrichmentPlot(
)
```
-
+
``` r
EnrichmentPlot(
@@ -543,7 +543,7 @@ EnrichmentPlot(
)
```
-
+
> To ensure that labels are visible, you can adjust the size of the
> viewer panel on Rstudio IDE.
@@ -555,13 +555,13 @@ EnrichmentPlot(
)
```
-
+
``` r
EnrichmentPlot(srt = pancreas_sub, group_by = "CellType", plot_type = "comparison")
```
-
+
### Enrichment analysis(GSEA)
@@ -573,7 +573,7 @@ pancreas_sub <- RunGSEA(
GSEAPlot(srt = pancreas_sub, group_by = "CellType", group_use = "Endocrine", id_use = "GO:0007186")
```
-
+
``` r
GSEAPlot(
@@ -582,13 +582,13 @@ GSEAPlot(
)
```
-
+
``` r
GSEAPlot(srt = pancreas_sub, group_by = "CellType", plot_type = "comparison")
```
-
+
### Trajectory inference
@@ -596,19 +596,19 @@ GSEAPlot(srt = pancreas_sub, group_by = "CellType", plot_type = "comparison")
pancreas_sub <- RunSlingshot(srt = pancreas_sub, group.by = "SubCellType", reduction = "UMAP")
```
-
+
``` r
FeatureDimPlot(pancreas_sub, features = paste0("Lineage", 1:3), reduction = "UMAP", theme_use = "theme_blank")
```
-
+
``` r
CellDimPlot(pancreas_sub, group.by = "SubCellType", reduction = "UMAP", lineages = paste0("Lineage", 1:3), lineages_span = 0.1)
```
-
+
### Dynamic features
@@ -627,7 +627,7 @@ ht <- DynamicHeatmap(
print(ht$plot)
```
-
+
``` r
DynamicPlot(
@@ -637,7 +637,7 @@ DynamicPlot(
)
```
-
+
``` r
FeatureStatPlot(
@@ -651,7 +651,7 @@ FeatureStatPlot(
)
```
-
+
### Interactive data visualization with SCExplorer
@@ -665,15 +665,15 @@ if (interactive()) {
}
```
-
-
+
+
### Other visualization examples
-[**CellDimPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellDimPlot.html)
-[**CellStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellStatPlot.html)
-[**FeatureStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/FeatureStatPlot.html)
-[**GroupHeatmap**](https://zhanghao-njmu.github.io/SCP/reference/GroupHeatmap.html)
+[**CellDimPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellDimPlot.html)
+[**CellStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/CellStatPlot.html)
+[**FeatureStatPlot**](https://zhanghao-njmu.github.io/SCP/reference/FeatureStatPlot.html)
+[**GroupHeatmap**](https://zhanghao-njmu.github.io/SCP/reference/GroupHeatmap.html)
You can also find more examples in the documentation of the function:
[Integration_SCP](https://zhanghao-njmu.github.io/SCP/reference/Integration_SCP.html),
diff --git a/inst/python/__pycache__/SCP_analysis.cpython-38.pyc b/inst/python/__pycache__/SCP_analysis.cpython-38.pyc
index bd20026c..c569e89c 100644
Binary files a/inst/python/__pycache__/SCP_analysis.cpython-38.pyc and b/inst/python/__pycache__/SCP_analysis.cpython-38.pyc differ
diff --git a/man/CellDimPlot3D.Rd b/man/CellDimPlot3D.Rd
index ec567841..ea32abe3 100644
--- a/man/CellDimPlot3D.Rd
+++ b/man/CellDimPlot3D.Rd
@@ -34,7 +34,7 @@ CellDimPlot3D(
\item{reduction}{Which dimensionality reduction to use. If not specified, will use the reduction returned by \code{\link{DefaultReduction}}.}
-\item{dims}{Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions}
+\item{dims}{Dimensions to plot, must be a three-length numeric vector specifying x-, y- and z-dimensions}
\item{axis_labs}{A character vector of length 3 indicating the labels for the axes.}
@@ -64,7 +64,7 @@ CellDimPlot3D(
\item{height}{Height in pixels, defaults to automatic sizing.}
-\item{save}{The name of the file to save the plot to. Must end in .html.}
+\item{save}{The name of the file to save the plot to. Must end in ".html".}
\item{force}{Whether to force drawing regardless of maximum levels in any cell group is greater than 100.}
}
@@ -78,6 +78,7 @@ CellDimPlot3D(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUM
pancreas_sub <- RunSlingshot(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUMAP3D")
CellDimPlot3D(pancreas_sub, group.by = "SubCellType", reduction = "StandardpcaUMAP3D", lineages = "Lineage1")
+
}
\seealso{
\code{\link{CellDimPlot}} \code{\link{FeatureDimPlot3D}}
diff --git a/man/Env_requirements.Rd b/man/Env_requirements.Rd
index 5b90e9e0..eb4d7b2f 100644
--- a/man/Env_requirements.Rd
+++ b/man/Env_requirements.Rd
@@ -4,7 +4,7 @@
\alias{Env_requirements}
\title{Env_requirements function}
\usage{
-Env_requirements(version = c("3.8-1", "3.8-2", "3.9-1", "3.10-1", "3.11-1"))
+Env_requirements(version = "3.8-1")
}
\arguments{
\item{version}{A character vector specifying the version of the environment (default is "3.8-1").}
diff --git a/man/FeatureDimPlot3D.Rd b/man/FeatureDimPlot3D.Rd
index 829e4cad..eb934425 100644
--- a/man/FeatureDimPlot3D.Rd
+++ b/man/FeatureDimPlot3D.Rd
@@ -58,7 +58,7 @@ FeatureDimPlot3D(
\item{height}{Height in pixels, defaults to automatic sizing.}
-\item{save}{The name of the file to save the plot to. Must end in .html.}
+\item{save}{The name of the file to save the plot to. Must end in ".html".}
\item{force}{Whether to force drawing regardless of the number of features greater than 100.}
}
diff --git a/man/Integration_SCP.Rd b/man/Integration_SCP.Rd
index adb53f82..3663c338 100644
--- a/man/Integration_SCP.Rd
+++ b/man/Integration_SCP.Rd
@@ -129,14 +129,18 @@ integration_methods <- c("Uncorrected", "Seurat", "scVI", "MNN", "fastMNN", "Har
for (method in integration_methods) {
panc8_sub <- Integration_SCP(
srtMerge = panc8_sub, batch = "tech",
- integration_method = method, linear_reduction_dims_use = 1:50, nonlinear_reduction = "umap"
+ integration_method = method,
+ linear_reduction_dims_use = 1:50,
+ nonlinear_reduction = "umap"
)
print(CellDimPlot(panc8_sub, group.by = c("tech", "celltype"), reduction = paste0(method, "UMAP2D"), theme_use = "theme_blank"))
}
nonlinear_reductions <- c("umap", "tsne", "dm", "phate", "pacmap", "trimap", "largevis", "fr")
panc8_sub <- Integration_SCP(
- srtMerge = panc8_sub, batch = "tech", integration_method = "Seurat",
+ srtMerge = panc8_sub, batch = "tech",
+ integration_method = "Seurat",
+ linear_reduction_dims_use = 1:50,
nonlinear_reduction = nonlinear_reductions
)
for (nr in nonlinear_reductions) {
diff --git a/man/check_R.Rd b/man/check_R.Rd
index cb942463..789f94f9 100644
--- a/man/check_R.Rd
+++ b/man/check_R.Rd
@@ -6,7 +6,6 @@
\usage{
check_R(
packages,
- package_names = NULL,
install_methods = c("BiocManager::install", "install.packages",
"devtools::install_github"),
lib = .libPaths()[1],
@@ -14,9 +13,7 @@ check_R(
)
}
\arguments{
-\item{packages}{Package to be installed. Package source can be CRAN, Bioconductor or Github, e.g. scmap, davidsjoberg/ggsankey.}
-
-\item{package_names}{The name of the package that corresponds to the \code{packages} parameter, used to check if the package is already installed.
+\item{packages}{Package to be installed. Package source can be CRAN, Bioconductor or Github, e.g. scmap, quadbiolab/simspec.
By default, the package name is extracted according to the \code{packages} parameter.}
\item{install_methods}{Functions used to install R packages.}
diff --git a/README/README-CellDimPlot3D-1.png b/man/figures/CellDimPlot3D-1.png
similarity index 100%
rename from README/README-CellDimPlot3D-1.png
rename to man/figures/CellDimPlot3D-1.png
diff --git a/README/README-DynamicHeatmap-1.png b/man/figures/DynamicHeatmap-1.png
similarity index 100%
rename from README/README-DynamicHeatmap-1.png
rename to man/figures/DynamicHeatmap-1.png
diff --git a/README/README-DynamicPlot-1.png b/man/figures/DynamicPlot-1.png
similarity index 100%
rename from README/README-DynamicPlot-1.png
rename to man/figures/DynamicPlot-1.png
diff --git a/README/README-EDA-1.png b/man/figures/EDA-1.png
similarity index 100%
rename from README/README-EDA-1.png
rename to man/figures/EDA-1.png
diff --git a/README/README-EDA-2.png b/man/figures/EDA-2.png
similarity index 100%
rename from README/README-EDA-2.png
rename to man/figures/EDA-2.png
diff --git a/README/README-EDA-3.png b/man/figures/EDA-3.png
similarity index 100%
rename from README/README-EDA-3.png
rename to man/figures/EDA-3.png
diff --git a/README/README-EDA-4.png b/man/figures/EDA-4.png
similarity index 100%
rename from README/README-EDA-4.png
rename to man/figures/EDA-4.png
diff --git a/README/README-EDA-5.png b/man/figures/EDA-5.png
similarity index 100%
rename from README/README-EDA-5.png
rename to man/figures/EDA-5.png
diff --git a/README/README-Enrichment_comparison-1.png b/man/figures/Enrichment_comparison-1.png
similarity index 100%
rename from README/README-Enrichment_comparison-1.png
rename to man/figures/Enrichment_comparison-1.png
diff --git a/README/README-Enrichment_enrichmap-1.png b/man/figures/Enrichment_enrichmap-1.png
similarity index 100%
rename from README/README-Enrichment_enrichmap-1.png
rename to man/figures/Enrichment_enrichmap-1.png
diff --git a/README/README-Example-1.jpg b/man/figures/Example-1.jpg
similarity index 100%
rename from README/README-Example-1.jpg
rename to man/figures/Example-1.jpg
diff --git a/README/README-Example-2.jpg b/man/figures/Example-2.jpg
similarity index 100%
rename from README/README-Example-2.jpg
rename to man/figures/Example-2.jpg
diff --git a/README/README-Example-3.jpg b/man/figures/Example-3.jpg
similarity index 100%
rename from README/README-Example-3.jpg
rename to man/figures/Example-3.jpg
diff --git a/README/README-Example-4.jpg b/man/figures/Example-4.jpg
similarity index 100%
rename from README/README-Example-4.jpg
rename to man/figures/Example-4.jpg
diff --git a/README/README-FeatureDimPlot3D-1.png b/man/figures/FeatureDimPlot3D-1.png
similarity index 100%
rename from README/README-FeatureDimPlot3D-1.png
rename to man/figures/FeatureDimPlot3D-1.png
diff --git a/README/README-FeatureHeatmap-1.png b/man/figures/FeatureHeatmap-1.png
similarity index 100%
rename from README/README-FeatureHeatmap-1.png
rename to man/figures/FeatureHeatmap-1.png
diff --git a/README/README-FeatureStatPlot-1.png b/man/figures/FeatureStatPlot-1.png
similarity index 100%
rename from README/README-FeatureStatPlot-1.png
rename to man/figures/FeatureStatPlot-1.png
diff --git a/README/README-GSEA_bar-1.png b/man/figures/GSEA_bar-1.png
similarity index 100%
rename from README/README-GSEA_bar-1.png
rename to man/figures/GSEA_bar-1.png
diff --git a/README/README-GSEA_comparison-1.png b/man/figures/GSEA_comparison-1.png
similarity index 100%
rename from README/README-GSEA_comparison-1.png
rename to man/figures/GSEA_comparison-1.png
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similarity index 100%
rename from README/README-Integration-all.png
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similarity index 100%
rename from README/README-Integration_SCP-1.png
rename to man/figures/Integration_SCP-1.png
diff --git a/README/README-RunCellQC-1.png b/man/figures/RunCellQC-1.png
similarity index 100%
rename from README/README-RunCellQC-1.png
rename to man/figures/RunCellQC-1.png
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rename from README/README-RunCellQC-3.png
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diff --git a/README/README-RunDEtest-1.png b/man/figures/RunDEtest-1.png
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rename from README/README-RunDEtest-1.png
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rename to man/figures/RunKNNMap-1.png
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diff --git a/README/README-Standard_SCP-1.png b/man/figures/Standard_SCP-1.png
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rename to man/figures/Standard_SCP-1.png