Add support for PlotAverageAdtCounts

Author: bbimber

singlecell/resources/chunks/PlotAverageCiteSeqCounts.R

@@ -0,0 +1,12 @@
+for (datasetId in names(seuratObjects)) {
+  seuratObj <- readRDS(seuratObjects[[datasetId]])
+
+  if (!('ADT' %in% names(seuratObj@assays))) {
+    print('ADT assay not present, skipping')
+  } else {
+    CellMembrane::PlotAverageAdtCounts(seuratObj, groupFields = fieldNames)
+  }
+
+  # Cleanup
+  rm(seuratObj)
+}

singlecell/src/org/labkey/singlecell/SingleCellModule.java

@@ -165,6 +165,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new SeuratPrototype.Provider());
         SequencePipelineService.get().registerPipelineStep(new DietSeurat.Provider());
         SequencePipelineService.get().registerPipelineStep(new ClearCommands.Provider());
+        SequencePipelineService.get().registerPipelineStep(new PlotAverageCiteSeqCounts.Provider());
 
         SequenceAnalysisService.get().registerFileHandler(new NimbleAlignmentStep());
     }

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

@@ -0,0 +1,57 @@
+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 org.labkey.api.util.PageFlowUtil;
+
+import java.util.Arrays;
+import java.util.Collection;
+
+public class PlotAverageCiteSeqCounts extends AbstractCellMembraneStep
+{
+    public PlotAverageCiteSeqCounts(PipelineContext ctx, PlotAverageCiteSeqCounts.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("PlotAverageCiteSeqCounts", "PlotAverageCiteSeqCounts", "CellMembrane", "This will generate a heatmap with average ADT counts, grouped using the fields below.", Arrays.asList(
+                    SeuratToolParameter.create("fieldNames", "Fields To Plot", "Enter one field name per line", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("allowBlank", false);
+                        put("height", 150);
+                        put("delimiter", ",");
+                    }}, "ClusterNames_0.2,ClusterNames_0.4,ClusterNames_0.6")
+            ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
+        }
+
+        @Override
+        public PlotAverageCiteSeqCounts create(PipelineContext ctx)
+        {
+            return new PlotAverageCiteSeqCounts(ctx, this);
+        }
+    }
+
+    @Override
+    public Collection<String> getRLibraries()
+    {
+        return PageFlowUtil.set("Seurat");
+    }
+
+    @Override
+    public boolean createsSeuratObjects()
+    {
+        return false;
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "avgAdt";
+    }
+}