Merge pull request #246 from samuel-marsh/release/3.2.1

Release/3.2.1

Author: samuel-marsh

.gitignore

@@ -3,7 +3,6 @@
 .RData
 .Ruserdata
 .DS_Store
-scCustomize.Rproj
 vignettes/assets
 README.Rmd
 index.Rmd

DESCRIPTION

@@ -2,8 +2,8 @@ Package: scCustomize
 Type: Package
 Title: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
 Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'.  'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions.  For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.
-Version: 3.2.0
-Date: 2025-09-09
+Version: 3.2.1
+Date: 2025-11-07
 Authors@R: c(
     person(given = "Samuel", family = "Marsh", email = "sccustomize@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3012-6945")),
     person(given = "Ming", family = "Tang", role = c("ctb"), email = "tangming2005@gmail.com"),
@@ -69,4 +69,4 @@ License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NAMESPACE

@@ -39,7 +39,6 @@ export(Add_Mito_Ribo)
 export(Add_Pct_Diff)
 export(Add_Sample_Meta)
 export(Add_Top_Gene_Pct)
-export(Add_Top_Gene_Pct_Seurat)
 export(Barcode_Plot)
 export(Blank_Theme)
 export(Case_Check)
@@ -70,6 +69,7 @@ export(DimPlot_LIGER)
 export(DimPlot_scCustom)
 export(DiscretePalette_scCustomize)
 export(DotPlot_scCustom)
+export(ElbowPlot_scCustom)
 export(Embeddings)
 export(Extract_Modality)
 export(Extract_Sample_Meta)
@@ -95,8 +95,8 @@ export(Iterate_Plot_Density_Custom)
 export(Iterate_Plot_Density_Joint)
 export(Iterate_VlnPlot_scCustom)
 export(JCO_Four)
-export(Liger_to_Seurat)
 export(MAD_Stats)
+export(Map_New_Meta)
 export(Median_Stats)
 export(Merge_Seurat_List)
 export(Merge_Sparse_Data_All)
@@ -291,6 +291,7 @@ importFrom(patchwork,plot_layout)
 importFrom(patchwork,wrap_plots)
 importFrom(pbapply,pblapply)
 importFrom(pbapply,pboptions)
+importFrom(purrr,compact)
 importFrom(purrr,discard)
 importFrom(purrr,keep)
 importFrom(purrr,map)

NEWS.md

@@ -1,3 +1,36 @@
+# scCustomize 3.2.1 (2025-11-07)  
+## Added  
+- Added new function `ElbowPlot_scCustom` which expands `ElbowPlot` to include calculations of amount of variance conferred by PCs.  See manual for more details.  
+- Added new function `Map_New_Meta` to enable mapping of existing meta.data column to new variable.  
+- Added `split_downsample` parameter to `DimPlot_scCustom` to downsample each group when splitting plots to the number of cells in the smallest group.  
+- Added `show_annotation_name` parameter to `Clustered_DotPlot` to control whether annotation name is shown next to color bar on plot. Thanks @Biase-lab, ([#243](https://github.com/samuel-marsh/scCustomize/issues/243)).  
+- Added `no_file_prefix` to `Read_CellBender_h5_Multi_Directory` to allow for situations where file does not share folder name as prefix, default is FALSE. Thanks @pedro-fr, ([#242](https://github.com/samuel-marsh/scCustomize/issues/242)).  
+- Added `columnns` parameter to `Fetch_Meta` to allow for return of select meta data columns instead of all columns (default remains returning all columns).  
+- Added support for VDJ B metrics in `Read_Metrics_10X`.  
+- Added support for Antibody Capture metrics in `Read_Metrics_10X`.  
+
+
+## Changed  
+- **BREAKING CHANGE** The `sample_name` parameter has been soft-deprecated in `Extract_Sample_Meta`.  Please use `sample_col` instead.  Using `sample_name` will warn user but still work until scCustomize v3.3.0.  
+- Updated messages in `Random_Cells_Downsample`.  
+- Full deprecation of `Add_Top_Gene_Pct_Seurat`, see current `Add_Top_Gene_Pct` function.  
+- Full deprecation of `Liger_to_Seurat` see `as.Seurat` for LIGER v1.0 objects or `rliger::ligerToSeurat` for LIGER v2.0+ objects.  
+- Updated `Iterate_Cluster_Highlight_Plot` to use consistent `pt.size` across all plots if `pt.size = NULL` in function call.  
+  
+
+
+## Fixes  
+- Fixed calculation of number of cells x number of features in `VlnPlot_scCustom` to properly rasterize plot if total is greater than 200,000.  Thanks @DavideBrex, ([#244](https://github.com/samuel-marsh/scCustomize/issues/244)).  
+- Fixed issue with `Read_Metrics_10X` for outputs when `cellranger_multi = TRUE` and Cell Ranger v9+ was used to process data.  Thanks @lisch7, ([#245](https://github.com/samuel-marsh/scCustomize/issues/245)).  
+- Fixed bug in `Proportion_Plot_per_Sample` due to missing parameter internally when pulling meta data and orig.ident did not represent sample IDs.  
+- Fixed bug in `Top_Genes_Factor` for LIGER objects when setting `factor = "all"`. Thanks @theAeon, ([#247](https://github.com/samuel-marsh/scCustomize/issues/247)).  
+- Fixed bug in `Update_HGNC_Symbols` due to error reading HGNC file.  Thanks @MD-Paris, ([#248](https://github.com/samuel-marsh/scCustomize/issues/248)).  
+- Fixed bug in `Variable_Features_ALL_LIGER` that didn't pass `num_genes` parameter correctly to LIGER v2+ objects.  
+  
+
+
+
+
 # scCustomize 3.2.0 (2025-09-09)  
 ## Added  
 - Added cNMF vignette.  

R/Color_Palettes.R

@@ -130,8 +130,6 @@ viridis_light_high <- as.vector(x = paletteer_c(palette = "viridis::viridis", n
 #' See RColorBrewer for more info on palettes
 #' \url{https://CRAN.R-project.org/package=RColorBrewer}
 #'
-#' @import cli
-#'
 #' @export
 #'
 #' @concept palettes
@@ -199,7 +197,7 @@ Single_Color_Palette <- function(
 #'
 #' Shortcut to navy orange color plot
 #'
-#' @param flip_order Whether to flip the order of colors.
+#' @param flip_order logical, whether to flip the order of colors.
 #'
 #' @return Navy orange palette
 #'
@@ -374,10 +372,8 @@ varibow_scCustom <- function(
 #' that is normally an ordered palette.
 #' @param seed random seed for the palette shuffle.  Default = 123.
 #'
-#' @import cli
 # #' @importFrom colorway varibow (now directly ported for CRAN compatibility)
 #' @importFrom paletteer paletteer_d
-#' @importFrom rlang is_installed
 #'
 #' @return A vector of colors
 #'
@@ -552,7 +548,6 @@ scCustomize_Palette <- function(
 #' @param 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.
 #'
-#' @import cli
 #' @import ggplot2
 #'
 #' @return Plot of all colors in supplied palette/vector
@@ -598,13 +593,13 @@ PalettePlot <- function(
   # Plot
   # Label plot
   if (isTRUE(x = label_color_num)) {
-    palette_plot <- ggplot(palette_data) +
+    palette_plot <- ggplot(data = palette_data) +
       geom_tile(aes(x = .data[["x"]], y = .data[["y"]], fill = .data[["fill"]])) +
       geom_text(aes(x = .data[["x"]], y = .data[["y"]], label = .data[["x"]])) +
       scale_fill_identity() +
       theme_void()
   } else {
-    palette_plot <- ggplot(palette_data) +
+    palette_plot <- ggplot(data = palette_data) +
       geom_tile(aes(x = .data[["x"]], y = .data[["y"]], fill = .data[["fill"]])) +
       scale_fill_identity() +
       theme_void()

R/Deprecated.R

@@ -77,16 +77,16 @@
 # }
 
 
-#' @description
-#' Use [Add_Top_Gene_Pct()] instead of `Add_Top_Gene_Pct_Seurat()`.
-#'
-#' @export
-#' @keywords internal
-#' @rdname deprecated
+# @description
+# Use [Add_Top_Gene_Pct()] instead of `Add_Top_Gene_Pct_Seurat()`.
+#
+# @export
+# @keywords internal
+# @rdname deprecated
 
-Add_Top_Gene_Pct_Seurat <- function(...) {
-  lifecycle::deprecate_stop(when = "2.2.0", what = "Add_Top_Gene_Pct_Seurat()", with = "Add_Top_Gene_Pct()", details = "Deprecation error when calling function will be removed in v3.1.0+")
-}
+# Add_Top_Gene_Pct_Seurat <- function(...) {
+#   lifecycle::deprecate_stop(when = "2.2.0", what = "Add_Top_Gene_Pct_Seurat()", with = "Add_Top_Gene_Pct()", details = "Deprecation error when calling function will be removed in v3.1.0+")
+# }
 
 # @description
 # Use [Feature_Present()] instead of `Gene_Present()`.

R/Generics.R

@@ -167,6 +167,7 @@ Add_Cell_QC_Metrics <- function(object, ...) {
 #' Quick function to properly pull meta.data from objects.
 #'
 #' @param object Object of class Seurat or liger.
+#' @param columns optional, name(s) of columns to return. Default is NULL; returns all columns
 #' @param ... Arguments passed to other methods
 #'
 #' @return A data.frame containing cell-level meta data
@@ -183,7 +184,7 @@ Add_Cell_QC_Metrics <- function(object, ...) {
 #' head(meta_data, 5)
 #'
 
-Fetch_Meta <- function(object, ...) {
+Fetch_Meta <- function(object, columns = NULL, ...) {
   UseMethod(generic = "Fetch_Meta", object = object)
 }