Update .HasNormalizationBeenPerformed for Assay5 inputs

BimberLab · Jan 30, 2024 · 9296b60 · 9296b60
1 parent 67687f0
commit 9296b60
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Showing 2 changed files with 11 additions and 4 deletions.
diff --git a/R/Phenotyping.R b/R/Phenotyping.R
@@ -91,7 +91,7 @@ PlotImmuneMarkers <- function(seuratObj, reductions = c('tsne', 'umap')) {
 	PlotMarkerSeries(seuratObj, reductions = reductions, features = c('HAVCR2'), 'Th1')
 
 	# ZBTB16 = PLZF
-	PlotMarkerSeries(seuratObj, reductions = reductions, features = c('KLRB1', 'NCR3', 'ZBTB16', 'RORC', 'SLC4A10', 'DPP4'), 'MAIT')
+	PlotMarkerSeries(seuratObj, reductions = reductions, features = c('KLRB1', 'CEPBD', 'NCR3', 'ZBTB16', 'RORC', 'SLC4A10', 'DPP4'), 'MAIT')
 
 	# ZNF683 = HOBIT
 	# LOC100423131 = XCL1, ENSMMUG00000013779, Lymphotactin

diff --git a/R/Utils.R b/R/Utils.R
@@ -92,11 +92,18 @@ SeuratToMatrix <- function(seuratObj, outDir, assayName, slot = 'counts'){
 }
 
 .HasNormalizationBeenPerformed <- function(seuratObj, assayName = Seurat::DefaultAssay(seuratObj)){
-    if (!assayName %in% names(seuratObj@assays)) {
-        stop(paste0('Assay not found: ', assayName))
-    }
+  if (!assayName %in% names(seuratObj@assays)) {
+    stop(paste0('Assay not found: ', assayName))
+  }
 
+  assayObj <- Seurat::GetAssay(seuratObj, assay = assayName)
+  if (class(assayObj)[1] == 'Assay') {
     return(!identical(Seurat::GetAssayData(seuratObj, assay = assayName, slot = 'counts'), Seurat::GetAssayData(seuratObj, assay = assayName, slot = 'data')))
+  } else if (class(assayData)[1] == 'Assay5') {
+    return('data' %in% names(assayObj@layers))
+  } else {
+    stop(paste0('Unknown assay class: ', class(assayData)[1]))
+  }
 }
 
 .FilterLowCalls <- function(seuratObj, label, minFraction, returnAsFactor = TRUE, labelToAssign = 'Unknown') {