Allow one to drop ambiguous calls in scGate

Author: bbimber

singlecell/resources/chunks/RunScGate.R

@@ -1,7 +1,7 @@
 for (datasetId in names(seuratObjects)) {
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, labelRename = list(Tcell = 'T_NK', NK = 'T_NK'))
+    seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, labelRename = list(Tcell = 'T_NK', NK = 'T_NK'), dropAmbiguousConsensusValues = dropAmbiguousConsensusValues)
 
     saveData(seuratObj, datasetId)
 }

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

@@ -28,8 +28,11 @@ public Provider()
                         put("initialValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Erythrocyte;Epithelial;Platelet_MK");
                         put("delimiter", ";");
                         put("joinReturnValue", true);
-                    }}, null, null, true, true)
-            ), null, null);
+                    }}, null, null, true, true),
+                    SeuratToolParameter.create("dropAmbiguousConsensusValues", "Drop Ambiguous Consensus Values", "If checked, any consensus calls that are ambiguous will be set to NA", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true)
+                    ), null, null);
         }
 
         @Override