Support ClrNormalizeByGroup

Author: bbimber

singlecell/resources/chunks/ClrNormalizeByGroup.R

@@ -0,0 +1,13 @@
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readRDS(seuratObjects[[datasetId]])
+    gc()
+
+    seuratObj <- CellMembrane::ClrNormalizeByGroup(seuratObj, groupingVar = groupingVar, assayName = assayName, targetAssayName = targetAssayName, margin = margin, minCellsPerGroup = minCellsPerGroup, calculatePerCellUCell = calculatePerCellUCell)
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -167,6 +167,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new FindMarkers.Provider());
         SequencePipelineService.get().registerPipelineStep(new MergeSeurat.Provider());
         SequencePipelineService.get().registerPipelineStep(new NormalizeAndScale.Provider());
+        SequencePipelineService.get().registerPipelineStep(new ClrNormalizeByGroup.Provider());
 
         SequencePipelineService.get().registerPipelineStep(new PrepareRawCounts.Provider());
 

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

@@ -0,0 +1,59 @@
+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 ClrNormalizeByGroup extends AbstractCellMembraneStep
+{
+    public ClrNormalizeByGroup(PipelineContext ctx, ClrNormalizeByGroup.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("ClrNormalizeByGroup", "CLR Normalize By Group", "CellMembrane/Seurat", "This will run standard Seurat CLR normalization on the desired assay, subsetting by group.", Arrays.asList(
+                    SeuratToolParameter.create("groupingVar", "Group Variable", "The variable on which to group.", "textfield", new JSONObject(){{
+                        put("allowBlank", false);
+                    }}, "cDNA_ID"),
+                    SeuratToolParameter.create("assayName", "Source Assay", "The source assay", "textfield", new JSONObject(){{
+                        put("allowBlank", false);
+                    }}, "ADT"),
+                    SeuratToolParameter.create("targetAssayName", "Target Assay", "The target assay. Will overwrite the source if blank.", "textfield", new JSONObject(){{
+
+                    }}, null),
+                    SeuratToolParameter.create("margin", "Margin", "Passing to NormalizeData. Either 1 or 2.", "ldk-integerfield", new JSONObject(){{
+                        put("allowBlank", false);
+                    }}, 1),
+                    SeuratToolParameter.create("minCellsPerGroup", "Min Cells Per Group", "Any group with fewer than this many cells will be dropped.", "ldk-integerfield", new JSONObject(){{
+
+                    }}, 20),
+                    SeuratToolParameter.create("calculatePerCellUCell", "Calculate Per Feature UCell ", "If checked, ScaleData will only be performed on VariableFeatures, which should dramatically reduce time and memory", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true)
+                    ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
+        }
+
+
+        @Override
+        public ClrNormalizeByGroup create(PipelineContext ctx)
+        {
+            return new ClrNormalizeByGroup(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "clrByGroup";
+    }
+}
+
+