Small improvements to CITE-seq plot step

Author: bbimber

singlecell/resources/chunks/CiteSeqPlots.R

@@ -2,25 +2,23 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    if (!('ADT' %in% names(seuratObj@assays))) {
-        print('ADT assay not present, skipping')
+    assayName <- 'ADT'
+    if (!(assayName %in% names(seuratObj@assays))) {
+        print(paste0('Assay: ', assayName, ' not present, skipping'))
     } else {
-        for (adt in rownames(seuratObj[['ADT']])) {
+        for (feat in rownames(seuratObj[[assayName]])) {
             tryCatch({
-                CellMembrane::FeaturePlotAcrossReductions(seuratObj, features = paste0('adt_', adt))
+                CellMembrane::FeaturePlotAcrossReductions(seuratObj, features = paste0(toLower(assayName), '_', feat))
             }, error = function(e){
                 warning(conditionMessage(e))
                 traceback()
-                message('ADTs:')
-                message(paste0(sort(rownames(seuratObj@assays$ADT)), collapse = ', '))
+                message('Features:')
+                message(paste0(sort(rownames(seuratObj@assays[[assayName]])), collapse = ', '))
                 stop(paste0('Error running FeaturePlotAcrossReductions for: ', datasetId))
             })
-
         }
     }
 
-    saveData(seuratObj, datasetId)
-
     # Cleanup
     rm(seuratObj)
     gc()

singlecell/src/org/labkey/singlecell/pipeline/singlecell/CiteSeqPlots.java

@@ -25,6 +25,12 @@ public CiteSeqPlots create(PipelineContext ctx)
         }
     }
 
+    @Override
+    public boolean createsSeuratObjects()
+    {
+        return false;
+    }
+
     @Override
     public String getFileSuffix()
     {