Add ability to create FeaturePlots in seurat pipeline

Author: bbimber

singlecell/resources/chunks/FeaturePlots.R

@@ -0,0 +1,26 @@
+for (datasetId in names(seuratObjects)) {
+    seuratObj <- seuratObjects[[datasetId]]
+    seuratObjects[[datasetId]] <- NULL
+
+    for (field in fieldNames) {
+        if (ncol(Seurat::FetchData(seuratObj, vars = c('ident', field))) != 2) {
+            next
+        }
+
+        P1 <- Seurat::FeaturePlot(seuratObj, features = c(field), reduction = 'tsne')
+        P2 <- Seurat::FeaturePlot(seuratObj, features = c(field), reduction = 'umap')
+
+        if ('wnn.umap' %in% names(seuratObj@reductions)) {
+            P3 <- Seurat::FeaturePlot(seuratObj, features = c(field), reduction = 'wnn.umap')
+            P1 <- P1 | P2 | P3
+        } else {
+            P1 <- P1 | P2
+        }
+
+        P1 <- P1 + patchwork::plot_annotation(title = field) + patchwork::plot_layout(guides = "collect")
+    }
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -155,6 +155,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new CiteSeqWnn.Provider());
         SequencePipelineService.get().registerPipelineStep(new AvgExpression.Provider());
         SequencePipelineService.get().registerPipelineStep(new DimPlots.Provider());
+        SequencePipelineService.get().registerPipelineStep(new FeaturePlots.Provider());
         SequencePipelineService.get().registerPipelineStep(new CiteSeqDimReduxPca.Provider());
         SequencePipelineService.get().registerPipelineStep(new CiteSeqPlots.Provider());
         SequencePipelineService.get().registerPipelineStep(new PhenotypePlots.Provider());

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

@@ -0,0 +1,58 @@
+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 org.labkey.api.util.PageFlowUtil;
+
+import java.util.Arrays;
+import java.util.Collection;
+
+public class FeaturePlots extends AbstractCellMembraneStep
+{
+    public FeaturePlots(PipelineContext ctx, FeaturePlots.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("FeaturePlots", "Create FeaturePlots", "Seurat", "This will generate FeaturePlots for each of the features/variables below. Any variable not present is skipped.", Arrays.asList(
+                    SeuratToolParameter.create("fieldNames", "Fields To Plot", "Enter one field name per line", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("allowBlank", false);
+                        put("height", 150);
+                        put("delimiter", ",");
+                    }}, null)
+            ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
+        }
+
+
+        @Override
+        public FeaturePlots create(PipelineContext ctx)
+        {
+            return new FeaturePlots(ctx, this);
+        }
+    }
+
+    @Override
+    public Collection<String> getRLibraries()
+    {
+        return PageFlowUtil.set("Seurat", "patchwork");
+    }
+
+    @Override
+    public boolean createsSeuratObjects()
+    {
+        return false;
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "featureplot";
+    }
+}