bf qQC.plots.BrainOrg

vertesy · Dec 2, 2024 · 1dea193 · 1dea193
1 parent c982cba
commit 1dea193
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Showing 2 changed files with 12 additions and 9 deletions.
diff --git a/R/Seurat.Utils.R b/R/Seurat.Utils.R
@@ -27,7 +27,7 @@
 #'
 #' @param obj A Seurat object to be processed.
 #' @param param.list A list of parameters used in the processing steps.
-#' @param update_gene_symbols A boolean indicating whether to update gene symbols from HGNC. Default: `TRUE`.
+#' @param update_gene_symbols A boolean indicating whether to update gene symbols from HGNC. Default: `FALSE`.
 #' @param add.meta.fractions A boolean indicating whether to add meta data for fractions of cells in each cluster. Default: `FALSE`.
 #' @param precompute A boolean indicating whether to compute steps: `FindVariableFeatures()`,
 #' `calc.q99.Expression.and.set.all.genes()`,  `ScaleData()` and `RunPCA()` Default: `TRUE`.
@@ -58,7 +58,7 @@
 #'
 #' @export
 processSeuratObject <- function(obj, param.list = p,
-                                update_gene_symbols = TRUE,
+                                update_gene_symbols = FALSE,
                                 add.meta.fractions = FALSE,
                                 precompute = TRUE,
                                 compute = TRUE,
@@ -111,7 +111,7 @@ processSeuratObject <- function(obj, param.list = p,
 
   if (update_gene_symbols) {
     message("------------------- UpdateGenesSeurat -------------------")
-    obj <- UpdateGenesSeurat(objj)
+    obj <- UpdateGenesSeurat(obj)
   }
 
   if (precompute | add.meta.fractions) {

diff --git a/R/Seurat.Utils.Visualization.R b/R/Seurat.Utils.Visualization.R
@@ -3040,20 +3040,23 @@ qQC.plots.BrainOrg <- function(
   message(" > Plotting qQC.plots.BrainOrg...")
 
   # Check that the QC markers are in the object
-  QC.Features.Found <- intersect(QC.Features, colnames(obj@meta.data))
+  QC.Features.Found <- intersect(QC.Features, union(colnames(obj@meta.data), rownames(obj)))
+  QC.Features.Found.in.meta <- intersect(QC.Features, colnames(obj@meta.data))
   n.found <- length(QC.Features.Found)
   message(kppws(n.found, " found: ", QC.Features.Found))
   stopifnot(n.found > 1)
 
 
   # Count the number of NAs in specified columns
-  na_counts <- sapply(X = obj@meta.data[, QC.Features.Found], function(x) sum(is.na(x)))
+  na_counts <- sapply(X = obj@meta.data[, QC.Features.Found.in.meta], function(x) sum(is.na(x)))
 
   # Raise a warning if there are any NAs
-  if (sum(na_counts) > 0) {
-    warning(sprintf("There are %d NA values found\n", na_counts),
-      immediate. = TRUE
-    )
+  if(length(na_counts)){
+    if (sum(na_counts) > 0) {
+      warning(sprintf("There are %d NA values found\n", na_counts),
+              immediate. = TRUE
+      )
+    }
   }
 
   px <- list(