Expose filterDisallowedClasses for UpdateSeuratPrototype

Author: bbimber

singlecell/resources/chunks/UpdateSeuratPrototype.R

@@ -26,7 +26,7 @@ for (datasetId in names(seuratObjects)) {
   }
 
   if (runRira) {
-    seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE, maxAllowedUnknown = maxAllowedUnknown)
+    seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE, maxAllowedUnknown = maxAllowedUnknown, filterDisallowedClasses = filterDisallowedClasses)
     seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE)
     seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE)
   }

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

@@ -64,6 +64,10 @@ public Provider()
                     {{
                         put("checked", false);
                     }}, false),
+                    SeuratToolParameter.create("filterDisallowedClasses", "Filter Disallowed Classes (RIRA)", "This applies to RIRA classification. If true, then cells will be filtered based on expression of common contaminants, such as RBC or platelet genes ", "checkbox", new JSONObject()
+                    {{
+                        put("checked", true);
+                    }}, true),
                     SeuratToolParameter.create("maxAllowedUnknown", "Max Allowed Unknown (RIRA)", "If provided, this step will throw an error is more than this fraction of cells fail the check for disallowed UCell combinations", "ldk-numberfield", new JSONObject()
                     {{
                         put("minValue", 0);