Skip NAs when plotting

bbimber · bbimber · commit ad655b7daf0d · 2021-06-04T08:57:43.000-07:00
diff --git a/singlecell/resources/chunks/DimPlots.R b/singlecell/resources/chunks/DimPlots.R
@@ -8,10 +8,10 @@ for (datasetId in names(seuratObjects)) {
             next
         }
 
-        if (length((unique(seuratObj@meta.data))) <= 1) {
+        if (length(unique(na.omit(seuratObj@meta.data[[field]]))) == 0) {
             next
         } else {
-            print(paste0('Object has one or fewer values, skipping: ', field))
+            print(paste0('Object has no non-NA values, skipping: ', field))
         }
 
         P1 <- Seurat::DimPlot(seuratObj, group.by = field, reduction = 'tsne')

Original file line number	Diff line number	Diff line change
`@@ -8,10 +8,10 @@ for (datasetId in names(seuratObjects)) {`
`8`	`8`	`next`
`9`	`9`	`}`
`10`	`10`
`11`		`- if (length((unique(seuratObj@meta.data))) <= 1) {`
	`11`	`+ if (length(unique(na.omit(seuratObj@meta.data[[field]]))) == 0) {`
`12`	`12`	`next`
`13`	`13`	`} else {`
`14`		`- print(paste0('Object has one or fewer values, skipping: ', field))`
	`14`	`+ print(paste0('Object has no non-NA values, skipping: ', field))`
`15`	`15`	`}`
`16`	`16`
`17`	`17`	`P1 <- Seurat::DimPlot(seuratObj, group.by = field, reduction = 'tsne')`