More reporting for RunDecoupler

Author: bbimber

singlecell/resources/chunks/RunDecoupler.R

@@ -3,6 +3,11 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
     seuratObj <- CellMembrane::RunDecoupleR(seuratObj)
+    if (!all(is.na(heatmapGroupingVars))) {
+      for (heatmapGroupingVar in heatmapGroupingVars) {
+        PlotTfData(seuratObj, groupField = heatmapGroupingVar)
+      }
+    }
 
     saveData(seuratObj, datasetId)
 

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

@@ -1,7 +1,9 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
+import org.json.JSONObject;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 
 import java.util.Arrays;
@@ -18,7 +20,13 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         public Provider()
         {
             super("RunDecoupler", "Run decoupleR", "decoupleR", "This will run decoupleR to score transcription factor enrichment.", Arrays.asList(
-
+                    SeuratToolParameter.create("heatmapGroupingVars", "Heatmap Grouping Vars", "Enter one field name per line, which will be used to generate a heatmap of results", "sequenceanalysis-trimmingtextarea", new JSONObject()
+                    {{
+                        put("allowBlank", true);
+                        put("height", 150);
+                        put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
+                    }}, "ClusterNames_0.2", null, true, true).delimiter(",")
             ), null, null);
         }