Add UCell argument

Author: bbimber

singlecell/resources/chunks/CalculateUCellScores.R

@@ -9,7 +9,7 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
     message(paste0('Loading dataset ', datasetId, ', with total cells: ', ncol(seuratObj)))
-    seuratObj <- RIRA::CalculateUCellScores(seuratObj, storeRanks = storeRanks, assayName = assayName, forceRecalculate = forceRecalculate, ncores = nCores)
+    seuratObj <- RIRA::CalculateUCellScores(seuratObj, storeRanks = storeRanks, assayName = assayName, forceRecalculate = forceRecalculate, ncores = nCores, dropAllExistingUcells = dropAllExistingUcells)
 
     saveData(seuratObj, datasetId)
 

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

@@ -23,13 +23,16 @@ public Provider()
         {
             super("CalculateUCellScores", "Calculate UCell Scores", "Seurat", "This will generate UCell scores for a set of pre-defined gene modules", Arrays.asList(
                     SeuratToolParameter.create("storeRanks", "Store Ranks", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
-                        put("checked", true);
+                        put("checked", false);
                     }}, true),
                     SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "textfield", new JSONObject(){{
 
                     }}, "RNA"),
                     SeuratToolParameter.create("forceRecalculate", "Force Recalculate", "If checked, the UCell score will always be re-calculated.", "checkbox", new JSONObject(){{
 
+                    }}, false),
+                    SeuratToolParameter.create("dropAllExistingUcells", "Drop Existing UCells?", "If checked, this will drop all columns ending in _UCell. This implies forceRecalculate.", "checkbox", new JSONObject(){{
+
                     }}, false)
             ), null, null);
         }