Support additional scRNA-seq tools

Author: bbimber

singlecell/resources/chunks/CustomUCell.R

@@ -14,7 +14,7 @@ for (datasetId in names(seuratObjects)) {
 
   seuratObj <- UCell::AddModuleScore_UCell(seuratObj, features = toCalculate, storeRanks = storeRanks, assay = assayName)
   for (n in names(toCalculate)) {
-    print(Seurat::FeaturePlot(seuratObj, features = paste0(n, '_UCell'), min.cutoff = 'q02', max.cuttoff = 'q98'))
+    print(Seurat::FeaturePlot(seuratObj, features = paste0(n, '_UCell'), min.cutoff = 'q02', max.cutoff = 'q98'))
   }
 
   saveData(seuratObj, datasetId)

singlecell/resources/chunks/RunCsCore.R

@@ -0,0 +1,12 @@
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- CellMembrane::RunCsCore(seuratObj, saveFile = 'cscoreResults.rds')
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

singlecell/resources/chunks/RunEscape.R

@@ -0,0 +1,12 @@
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- CellMembrane::RunEscape(seuratObj, outputAssayName = outputAssayName, doPlot = TRUE)
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -226,6 +226,8 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new ScoreCellCycle.Provider());
         SequencePipelineService.get().registerPipelineStep(new TrainScTour.Provider());
         SequencePipelineService.get().registerPipelineStep(new PredictScTour.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunEscape.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunCsCore.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

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

@@ -0,0 +1,38 @@
+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;
+import java.util.Collections;
+
+public class RunCsCore extends AbstractCellMembraneStep
+{
+    public RunCsCore(PipelineContext ctx, Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunCsCore", "CS-CORE", "CS-CORE", "Run CS-CORE on the seurat object to identify gene modules.", Collections.emptyList(), null, null);
+        }
+
+        @Override
+        public RunCsCore create(PipelineContext ctx)
+        {
+            return new RunCsCore(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "cscore";
+    }
+}

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

@@ -0,0 +1,42 @@
+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;
+import java.util.Collections;
+
+public class RunEscape extends AbstractCellMembraneStep
+{
+    public RunEscape(PipelineContext ctx, Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunEscape", "Escape/ssGSEA", "escape", "Runs escape to perform ssGSEA using Hallmark gene sets.", Arrays.asList(
+                    SeuratToolParameter.create("outputAssayName", "Output Assay Name", "The name of the assay to store results", "textfield", new JSONObject(){{
+                        put("allowBank", false);
+                    }}, "escape.ssGSEA")
+            ), null, null);
+        }
+
+        @Override
+        public RunEscape create(PipelineContext ctx)
+        {
+            return new RunEscape(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "escape";
+    }
+}