Release/3.2.2

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: 3.2.1
-Date: 2025-11-07
+Version: 3.2.2
+Date: 2025-11-12
 Authors@R: c(
     person(given = "Samuel", family = "Marsh", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3012-6945")),
     person(given = "Ming", family = "Tang", role = c("ctb"), email = "[email protected]"),

NEWS.md

@@ -1,3 +1,24 @@
+# scCustomize 3.2.2 (2025-11-12)  
+## Added  
+
+
+
+## Changed  
+- Changed behavior of file extension checking in `Add_MALAT1_Threshold`.  
+
+
+
+## Fixes  
+- Fixed problem with `Add_Cell_QC_Metrics` that was not correctly accounting for all lncRNA genes when calculating percentage of lncRNA counts.  
+
+
+
+
+
+
+
+
+
 # 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.  

R/Internal_Utilities.R

@@ -1682,8 +1682,6 @@ Add_IEG_Seurat <- function(
 #' @param seurat_object object name.
 #' @param species Species of origin for given Seurat Object.
 #' @param lncRNA_name name to use for the new meta.data column containing percent lncRNA gene counts. Default is "percent_lncRNA".
-#' @param 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).
 #' @param assay Assay to use (default is the current object default assay).
 #' @param overwrite Logical.  Whether to overwrite existing meta.data columns.  Default is FALSE meaning that
 #' function will abort if columns with the name provided to `lncRNA_name` is present in meta.data slot.
@@ -1699,7 +1697,6 @@ Add_lncRNA_Seurat <- function(
     seurat_object,
     species,
     lncRNA_name = "percent_lncRNA",
-    ensembl_ids = FALSE,
     assay = NULL,
     overwrite = FALSE
 ) {
@@ -1738,13 +1735,9 @@ Add_lncRNA_Seurat <- function(
   assay <- assay %||% DefaultAssay(object = seurat_object)
 
   # Retrieve gene lists
-  if (isFALSE(x = ensembl_ids)) {
-    lncRNA_gene_list <- Retrieve_lncRNA(species = species)
-  } else {
-    lncRNA_gene_list <- Retrieve_Ensembl_lncRNA(species = species)
-  }
+  complete_lnc_list <- c(Retrieve_lncRNA(species = species), Retrieve_Ensembl_lncRNA(species = species))
 
-  lncRNA_found <- Feature_PreCheck(object = seurat_object, features = lncRNA_gene_list, print_missing = FALSE)
+  lncRNA_found <- Feature_PreCheck(object = seurat_object, features = complete_lnc_list, print_missing = FALSE)
 
   # Add mito and ribo columns
   if (length(x = lncRNA_found) > 0) {
@@ -1759,7 +1752,6 @@ Add_lncRNA_Seurat <- function(
 }
 
 
-
 #' Define MALAT1 QC Threshold
 #'
 #' This function is a threshold calculation and procedure as described in

R/LIGER_Internal_Utilities.R

@@ -2296,8 +2296,6 @@ Add_IEG_LIGER <- function(
 #' @param liger_object object name.
 #' @param species Species of origin for given Seurat Object.
 #' @param lncRNA_name name to use for the new meta.data column containing percent lncRNA gene counts. Default is "percent_lncRNA".
-#' @param 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).
 #' @param overwrite Logical.  Whether to overwrite existing meta data columns.  Default is FALSE meaning that
 #' function will abort if columns with the name provided to `lncRNA_name` is present in meta data slot.
 #'
@@ -2312,7 +2310,6 @@ Add_lncRNA_LIGER <- function(
     liger_object,
     species,
     lncRNA_name = "percent_lncRNA",
-    ensembl_ids = FALSE,
     overwrite = FALSE
 ) {
   # Accepted species names
@@ -2349,15 +2346,11 @@ Add_lncRNA_LIGER <- function(
   }
 
   # Retrieve gene lists
-  if (isFALSE(x = ensembl_ids)) {
-    lncRNA_gene_list <- Retrieve_lncRNA(species = species)
-  } else {
-    lncRNA_gene_list <- Retrieve_Ensembl_lncRNA(species = species)
-  }
+  complete_lnc_list <- c(Retrieve_lncRNA(species = species), Retrieve_Ensembl_lncRNA(species = species))
 
   all_features <- Features(x = liger_object, by_dataset = FALSE)
 
-  lncRNA_found <- intersect(x = lncRNA_gene_list, y = all_features)
+  lncRNA_found <- intersect(x = complete_lnc_list, y = all_features)
 
   # Add ieg column
   if (length(x = lncRNA_found) > 0) {

R/LIGER_Utilities.R

@@ -1197,16 +1197,12 @@ Add_Cell_QC_Metrics.liger <- function(
 
   # Add lncRNA
   if (isTRUE(x = add_lncRNA)) {
-    if (species %in% marmoset_options && isFALSE(x = ensembl_ids)) {
-      cli_warn(message = c("{.val Marmoset} lncRNAs do not currently have annotated symbols (only Ensembl IDs) in Ensembl database.",
-                           "i" = "No columns will be added to object meta.data"))
-    }
     if (species %in% drosophila_options) {
       cli_warn(message = c("{.val Drosophila} do not have separate lncRNA gene biotype (only ncRNA) in Ensembl database.",
                            "i" = "No columns will be added to object meta.data"))
     } else {
       cli_inform(message = c("*" = "Adding {.field lncRNA Percentages} to meta.data."))
-      object <- Add_lncRNA_LIGER(liger_object = object, species = species, lncRNA_name = lncRNA_name, overwrite = overwrite, ensembl_ids = ensembl_ids)
+      object <- Add_lncRNA_LIGER(liger_object = object, species = species, lncRNA_name = lncRNA_name, overwrite = overwrite)
     }
   }
 

R/QC_Utilities_Seurat.R

@@ -202,16 +202,12 @@ Add_Cell_QC_Metrics.Seurat <- function(
 
   # Add lncRNA
   if (isTRUE(x = add_lncRNA)) {
-    if (species %in% marmoset_options && isFALSE(x = ensembl_ids)) {
-      cli_warn(message = c("{.val Marmoset} lncRNAs do not currently have annotated symbols (only Ensembl IDs) in Ensembl database.",
-                           "i" = "No columns will be added to object meta.data"))
-    }
     if (species %in% drosophila_options) {
       cli_warn(message = c("{.val Drosophila} do not have separate lncRNA gene biotype (only ncRNA) in Ensembl database.",
                            "i" = "No columns will be added to object meta.data"))
     } else {
       cli_inform(message = c("*" = "Adding {.field lncRNA Percentages} to meta.data."))
-      object <- Add_lncRNA_Seurat(seurat_object = object, species = species, lncRNA_name = lncRNA_name, assay = assay, overwrite = overwrite, ensembl_ids = ensembl_ids)
+      object <- Add_lncRNA_Seurat(seurat_object = object, species = species, lncRNA_name = lncRNA_name, assay = assay, overwrite = overwrite)
     }
   }
 
@@ -1099,7 +1095,7 @@ Add_MALAT1_Threshold.Seurat <- function(
     # append .pdf if needed
     file_ext <- grep(x = save_plot_name, pattern = ".pdf$")
     if (length(x = file_ext) == 0) {
-      cli_abort(message = "{.code save_plot_name} must end with file extension '.pdf'.")
+      save_plot_name <- paste0(save_plot_name, ".pdf")
     }
 
     # check non-default output values

cran-comments.md

@@ -1,5 +1,5 @@
 ## Update 
-This is minor update to version 3.2.1.  Contains bug fixes and 2 new functions.  See News.md for full changelog.  
+This is minor patch to version 3.2.2.  Contains 2 critical bug fixes.  See News.md for full changelog.