Add option to drop assays in seurat objects on merge

Author: bbimber

singlecell/resources/chunks/MergeSeurat.R

@@ -12,6 +12,17 @@ mergeBatch <- function(dat) {
         }
     }
 
+    if (!is.null(assaysToDrop)) {
+        for (assayName in assaysToDrop) {
+            print(paste0('Dropping assay: ', assayName))
+            for (datasetId in names(toMerge)) {
+                if (assayName %in% names(toMerge[[datasetId]]@assays)) {
+                    toMerge[[datasetId]]@assays[[assayName]] <- NULL
+                }
+            }
+        }
+    }
+
     seuratObj <- CellMembrane::MergeSeuratObjs(toMerge, projectName = projectName, doGC = doDiet, errorOnBarcodeSuffix = errorOnBarcodeSuffix)
     return(seuratObj)
 }

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

@@ -28,7 +28,11 @@ public Provider()
                         put("allowBlank", false);
                     }}, null),
                     SeuratToolParameter.create("doDiet", "Run DietSeurat", "If selected, this will run DietSeurat and gc() on the incoming seurat objects prior to merge. This is primarily to help with memory.", "checkbox", null, false, "dietSeurat", true, false),
-                    SeuratToolParameter.create("errorOnBarcodeSuffix", "Error On Cell Barcode Suffixes", "In certain cases, software appends a digit (i.e. -1) to the end of cell barcodes; however, no code in DISCVR should do this. These are a problem if different datasets are inconsistent when using them.  If this setting is checked, the code will error if these are encountered.", "checkbox", null, true, "errorOnBarcodeSuffix", true, false)
+                    SeuratToolParameter.create("errorOnBarcodeSuffix", "Error On Cell Barcode Suffixes", "In certain cases, software appends a digit (i.e. -1) to the end of cell barcodes; however, no code in DISCVR should do this. These are a problem if different datasets are inconsistent when using them.  If this setting is checked, the code will error if these are encountered.", "checkbox", null, true, "errorOnBarcodeSuffix", true, false),
+                    SeuratToolParameter.create("assaysToDrop", "Assays to Drop", "These assays, entered comma-separated or one/line, will be dropped prior to merge.", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("height", 150);
+                        put("delimiter", ",");
+                    }}, "RNA.orig").delimiter(",")
             ), null, null);
         }