Support minFractionCloneActivated

Author: bbimber

singlecell/resources/chunks/ApplyKnownClonotypicData.R

@@ -11,7 +11,7 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- ApplyKnownClonotypicData(seuratObj, antigenInclusionList = antigenInclusionList, antigenExclusionList = antigenExclusionList, minActivationFrequency = minActivationFrequency)
+    seuratObj <- ApplyKnownClonotypicData(seuratObj, antigenInclusionList = antigenInclusionList, antigenExclusionList = antigenExclusionList, minActivationFrequency = minActivationFrequency, minFractionCloneActivated = minFractionCloneActivated)
     saveData(seuratObj, datasetId)
 
     # Cleanup

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

@@ -38,7 +38,12 @@ public Provider()
                         put("minValue", 0);
                         put("maxValue", 1.0);
                         put("decimalPrecision", 4);
-                    }}, 0)
+                    }}, 0.0005),
+                    SeuratToolParameter.create("minFractionCloneActivated", "Min Fraction Clone Activated", "If provided, only responses where the fraction of cells harboring that clone were activated will be included", "ldk-numberfield", new JSONObject(){{
+                        put("minValue", 0);
+                        put("maxValue", 1.0);
+                        put("decimalPrecision", 4);
+                    }}, 0.05)
             ), List.of("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }