Improve handling of RIRA filters

Author: bbimber

singlecell/resources/chunks/UpdateSeuratPrototype.R

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

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

@@ -28,12 +28,12 @@ public Provider()
                     {{
                         put("checked", true);
                     }}, true),
-                    SeuratToolParameter.create("maxAllowedUnknown", "Max Allowed Unknown", "If provided, ", "ldk-numberfield", new JSONObject()
+                    SeuratToolParameter.create("maxAllowedUnknown", "Max Allowed Unknown", "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);
                         put("maxValue", 1);
                         put("decimalPrecision", 2);
-                    }}, true)
+                    }}, 0.1)
             ), null, null);
         }
 

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

@@ -63,7 +63,13 @@ public Provider()
                     SeuratToolParameter.create("keepOriginal", "Keep Copy of Original File", "If checked, the original file will be copied with the file extension '.bk'", "checkbox", new JSONObject()
                     {{
                         put("checked", false);
-                    }}, false)
+                    }}, false),
+                    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);
+                        put("maxValue", 1);
+                        put("decimalPrecision", 2);
+                    }}, 0.1)
             ), null, null);
         }