Improve logic for HTO filtering

bbimber · bbimber · commit 811f2afe2a23 · 2022-03-30T12:27:37.000-07:00
diff --git a/singlecell/resources/chunks/CommonFilters.R b/singlecell/resources/chunks/CommonFilters.R
@@ -96,7 +96,7 @@ for (datasetId in names(seuratObjects)) {
 		}
 
 		tryCatch({
-			cells <- Seurat::WhichCells(seuratObj, expression = HTO.Classification!='ND' & HTO.Classification!='Discordant' & HTO.Classification!='Doublet')
+			cells <- Seurat::WhichCells(seuratObj, expression = HTO.Classification!='ND' & HTO.Classification!='Discordant' & HTO.Classification!='Doublet' & HTO.Classification!='Low Counts')
 			if (length(cells) == 0) {
 				print(paste0('There were no cells remaining after dropping cells without hashing'))
 				seuratObj <- NULL

Original file line number	Diff line number	Diff line change
`@@ -96,7 +96,7 @@ for (datasetId in names(seuratObjects)) {`
`96`	`96`	`}`
`97`	`97`
`98`	`98`	`tryCatch({`
`99`		`- cells <- Seurat::WhichCells(seuratObj, expression = HTO.Classification!='ND' & HTO.Classification!='Discordant' & HTO.Classification!='Doublet')`
	`99`	`+ cells <- Seurat::WhichCells(seuratObj, expression = HTO.Classification!='ND' & HTO.Classification!='Discordant' & HTO.Classification!='Doublet' & HTO.Classification!='Low Counts')`
`100`	`100`	`if (length(cells) == 0) {`
`101`	`101`	`print(paste0('There were no cells remaining after dropping cells without hashing'))`
`102`	`102`	`seuratObj <- NULL`