Support AvgExpression single cell step

Author: bbimber

singlecell/resources/chunks/AvgExpression.R

@@ -0,0 +1,16 @@
+for (datasetId in names(seuratObjects)) {
+    seuratObj <- seuratObjects[[datasetId]]
+    seuratObjects[[datasetId]] <- NULL
+
+    ret <- Seurat::AverageExpression(seuratObj, assays = NULL, features = rownames(seuratObj), group.by = groupField, slot = "counts", verbose = FALSE)
+    cellsPerGroup <- t(as.matrix(table(seuratObj[[assay]][[groupField]])))
+    rownames(cellsPerGroup) <- 'TotalCells'
+    ret[['CellsPerGroup']] <- cellsPerGroup
+
+    saveFile <- paste0(outputPrefix, '.', datasetId, '.avg.', groupField, '.rds')
+    saveRDS(ret, file = saveFile)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -41,6 +41,7 @@
 import org.labkey.singlecell.button.CellHashingButton;
 import org.labkey.singlecell.button.CiteSeqButton;
 import org.labkey.singlecell.pipeline.singlecell.AppendCiteSeq;
+import org.labkey.singlecell.pipeline.singlecell.AvgExpression;
 import org.labkey.singlecell.pipeline.singlecell.CiteSeqDimRedux;
 import org.labkey.singlecell.pipeline.singlecell.CiteSeqWnn;
 import org.labkey.singlecell.pipeline.singlecell.DoubletFinder;
@@ -176,6 +177,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new SubsetSeurat.Provider());
         SequencePipelineService.get().registerPipelineStep(new CiteSeqDimRedux.Provider());
         SequencePipelineService.get().registerPipelineStep(new CiteSeqWnn.Provider());
+        SequencePipelineService.get().registerPipelineStep(new AvgExpression.Provider());
     }
 
     @Override

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

@@ -0,0 +1,36 @@
+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 AvgExpression extends AbstractCellMembraneStep
+{
+    public AvgExpression(PipelineContext ctx, AvgExpression.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("AvgExpression", "Avg. Expression", "Seurat", "This will run AverageExpression on the raw counts, producing a matrix with the average per group. This matrix will have a row labeled TotalCells appended, which is the total cells per group.", Arrays.asList(
+                    SeuratToolParameter.create("groupField", "Grouping Field", "This field will be used to group cells of the seurat object. For each unique value of this field, count averages will be computed and saved into a matrix with one column per group. Any cells lacking a value in this field will be discarded.", "textfield", new JSONObject(){{
+                        put("allowBlank", false);
+                    }}, null)
+            ), null, null);
+        }
+
+        @Override
+        public AvgExpression create(PipelineContext ctx)
+        {
+            return new AvgExpression(ctx, this);
+        }
+    }
+}
+