Support more clonotype filters

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)
+    seuratObj <- ApplyKnownClonotypicData(seuratObj, antigenInclusionList = antigenInclusionList, antigenExclusionList = antigenExclusionList, minActivationFrequency = minActivationFrequency)
     saveData(seuratObj, datasetId)
 
     # Cleanup

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

@@ -33,7 +33,12 @@ public Provider()
                         put("delimiter", ",");
                         put("stripCharsRe", "/['\"]/g");
                         put("replaceAllWhitespace", false);
-                    }}, null, null, true, true).delimiter(",")
+                    }}, null, null, true, true).delimiter(","),
+                    SeuratToolParameter.create("minActivationFrequency", "Minimum Activation Frequency", "If provided, only responses with an activation frequency (of the parent population), will be included", "ldk-numberfield", new JSONObject(){{
+                        put("minValue", 0);
+                        put("maxValue", 1.0);
+                        put("decimalPrecision", 4);
+                    }}, 0)
             ), List.of("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }