Add support for PHATE

Author: bbimber

singlecell/resources/chunks/RunPHATE.R

@@ -0,0 +1,12 @@
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- CellMembrane::RunPHATE(seuratObj)
+    print(DimPlot(seuratObj, reduction = 'phate'))
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+}

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

@@ -173,6 +173,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new RemoveCellCycle.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunCellHashing.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunPCA.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunPHATE.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunSingleR.Provider());
         SequencePipelineService.get().registerPipelineStep(new FindClustersAndDimRedux.Provider());
         SequencePipelineService.get().registerPipelineStep(new SplitSeurat.Provider());

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

@@ -0,0 +1,41 @@
+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;
+
+public class RunPHATE extends AbstractCellMembraneStep
+{
+    public RunPHATE(PipelineContext ctx, RunPHATE.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunPHATE", "Run PHATE", "CellMembrane/phateR", "This will run PHATE on the input object.", Arrays.asList(
+
+            ), null, null);
+        }
+
+
+        @Override
+        public RunPHATE create(PipelineContext ctx)
+        {
+            return new RunPHATE(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "phate";
+    }
+}
+