Add step to generate phenotype plots

Author: bbimber

singlecell/resources/chunks/PhenotypePlots.R

@@ -0,0 +1,10 @@
+for (datasetId in names(seuratObjects)) {
+    seuratObj <- seuratObjects[[datasetId]]
+    seuratObjects[[datasetId]] <- NULL
+
+    CellMembrane::PlotImmuneMarkers(seuratObj)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -157,6 +157,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new DimPlots.Provider());
         SequencePipelineService.get().registerPipelineStep(new CiteSeqDimReduxPca.Provider());
         SequencePipelineService.get().registerPipelineStep(new CiteSeqPlots.Provider());
+        SequencePipelineService.get().registerPipelineStep(new PhenotypePlots.Provider());
     }
 
     @Override

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

@@ -0,0 +1,51 @@
+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 PhenotypePlots extends AbstractCellMembraneStep
+{
+    public PhenotypePlots(PipelineContext ctx, PhenotypePlots.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("PhenotypePlots", "Create Phenotype Plots", "Seurat", "This will generate FeaturePlots for a pre-defined set of immune markers. Any feature not present is skipped.", null, Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
+        }
+
+        @Override
+        public PhenotypePlots create(PipelineContext ctx)
+        {
+            return new PhenotypePlots(ctx, this);
+        }
+    }
+
+    @Override
+    public Collection<String> getRLibraries()
+    {
+        return PageFlowUtil.set("Seurat", "patchwork");
+    }
+
+    @Override
+    public boolean createsSeuratObjects()
+    {
+        return false;
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "phenotype";
+    }
+}