Bugfixes to cell hashing assignment

Author: bbimber

singlecell/resources/chunks/CommonFilters.R

@@ -95,6 +95,12 @@ for (datasetId in names(seuratObjects)) {
 			stop('Missing field: HTO.Classification')
 		}
 
+		# NOTE: this is added to fix an edge case that could occur if hashing not properly set
+		if (all(is.na(seuratObj$HTO.Classification))) {
+			print('HTO.Classification was NA, setting to NotUsed')
+			seuratObj$HTO.Classification <- 'NotUsed'
+		}
+
 		tryCatch({
 			cells <- Seurat::WhichCells(seuratObj, expression = HTO.Classification!='ND' & HTO.Classification!='Discordant' & HTO.Classification!='Doublet' & HTO.Classification!='Low Counts')
 			if (length(cells) == 0) {

singlecell/resources/chunks/SeuratPrototype.R

@@ -32,13 +32,8 @@ for (datasetId in names(seuratObjects)) {
     metricData <- rbind(metricData, data.frame(dataId = datasetId, readsetId = datasetIdToReadset[[datasetId]], metricname = 'FractionDiscordantHashing', metricvalue = fractionDiscordantHashing))
   } else {
     # Ensure these fields exist:
-    if (!'HTO.Classification' %in% names(seuratObj@meta.data)) {
-      seuratObj$HTO.Classification <- c('NotUsed')
-    }
-
-    if (!'HTO' %in% names(seuratObj@meta.data)) {
-      seuratObj$HTO <- c('NotUsed')
-    }
+    seuratObj$HTO.Classification <- c('NotUsed')
+    seuratObj$HTO <- c('NotUsed')
   }
 
   if (is.null(usesCiteSeq[[datasetId]])) {