Add step for custom gene sets and ssGSEA

Author: bbimber

singlecell/resources/chunks/CustomGSEA.R

@@ -0,0 +1,22 @@
+for (datasetId in names(seuratObjects)) {
+  printName(datasetId)
+  seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+  toCalculate <- list()
+  for (geneSet in geneSets) {
+    vals <- unlist(strsplit(geneSet, split = ':'))
+    if (length(vals) != 2) {
+      stop(paste0('Improper gene set: ', geneSet))
+    }
+
+    toCalculate[[vals[1]]] <- unlist(strsplit(vals[2], split = ','))
+  }
+
+  seuratObj <- CellMembrane::RunEscape(seuratObj, customGeneSets = toCalculate, outputAssayName = outputAssayName, doPlot = TRUE, msigdbGeneSets = NULL)
+
+  saveData(seuratObj, datasetId)
+
+  # Cleanup
+  rm(seuratObj)
+  gc()
+}

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

@@ -228,6 +228,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new PredictScTour.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunEscape.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunCsCore.Provider());
+        SequencePipelineService.get().registerPipelineStep(new CustomGSEA.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

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

@@ -0,0 +1,50 @@
+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.List;
+
+public class CustomGSEA extends AbstractCellMembraneStep
+{
+    final static String DELIM = "<>";
+
+    public CustomGSEA(PipelineContext ctx, CustomGSEA.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("CustomUCell", "ssGSEA (Custom)", "escape/ssGSEA", "The seurat object will be subset based on the expression below, which is passed directly to Seurat's subset(subset = X).", Arrays.asList(
+                    SeuratToolParameter.create("geneSets", "Gene Sets(s)", "This should contain one gene module per line, where the module is in the format (no spaces): SetName:Gene1,Gene2,Gene3. The first token is the name given to the score and the second is a comma-delimited list of gene names.", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("allowBlank", false);
+                        put("replaceAllWhitespace", true);
+                        put("height", 150);
+                        put("width", 600);
+                        put("delimiter", DELIM);
+                        put("stripCharsRe", "/['\"]/g");
+                    }}, null).delimiter(DELIM),
+                    SeuratToolParameter.create("assayName", "Input Assay Name", "The assay holding the source data.", "textfield", new JSONObject(){{
+                        put("allowBlank", false);
+                    }}, "RNA"),
+                    SeuratToolParameter.create("outputAssayName", "Output Assay Name", "The assay to hold the resulting scores.", "textfield", new JSONObject(){{
+                        put("allowBlank", false);
+                    }}, "escape.ssGSEA")
+            ), List.of("/sequenceanalysis/field/TrimmingTextArea.js"), null);
+        }
+
+
+        @Override
+        public CustomGSEA create(PipelineContext ctx)
+        {
+            return new CustomGSEA(ctx, this);
+        }
+    }
+}

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

@@ -23,7 +23,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("CustomUCell", "UCell (Custom)", "UCell/RIRA", "The seurat object will be subset based on the expression below, which is passed directly to Seurat's subset(subset = X).", Arrays.asList(
+            super("CustomUCell", "UCell (Custom)", "UCell/RIRA", "UCell scores will be calculated, based on the custom gene list below", Arrays.asList(
                     SeuratToolParameter.create("geneSets", "Gene Sets(s)", "This should contain one UCell module per line, where the module is in the format (no spaces): SetName:Gene1,Gene2,Gene3. The first token is the name given to UCell and the second is a comma-delimited list of gene names.", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("allowBlank", false);
                         put("replaceAllWhitespace", true);