Add step to plot features across arbitrary assays

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java

@@ -109,7 +109,7 @@ public Collection<String> getAllowableActionNames()
     {
         Set<String> allowableNames = new HashSet<>();
         allowableNames.add(getName());
-        for (PipelineStepProvider provider: SequencePipelineService.get().getProviders(VariantProcessingStep.class))
+        for (PipelineStepProvider<?> provider: SequencePipelineService.get().getProviders(VariantProcessingStep.class))
         {
             allowableNames.add(provider.getLabel());
         }

singlecell/resources/chunks/PlotAssayFeatures.R

@@ -0,0 +1,37 @@
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readRDS(seuratObjects[[datasetId]])
+
+    for (assayName in assayNames) {
+        print(paste0('Processing assay: ', assayName))
+        featureNames <- rownames(seuratObj@assays[assayName])
+        if (length(featureNames) > 100) {
+            warning(paste0('There are too many features in this assay, skipping: ', assayName))
+            next
+        }
+
+        for (featureName in featureNames) {
+            if (ncol(Seurat::FetchData(seuratObj, vars = c('ident', featureName))) != 2) {
+                next
+            }
+
+            tryCatch({
+                P1 <- Seurat::FeaturePlot(seuratObj, features = c(featureName), reduction = 'tsne', min.cutoff = 'q05', max.cutoff = 'q95')
+                P2 <- Seurat::FeaturePlot(seuratObj, features = c(featureName), reduction = 'umap', min.cutoff = 'q05', max.cutoff = 'q95')
+                P1 <- P1 | P2
+
+                P1 <- P1 + patchwork::plot_annotation(title = featureName) + patchwork::plot_layout(guides = "collect")
+
+                print(P1)
+            }, error = function(e){
+                print(paste0('Error running NimbleFeaturePlots for: ', datasetId))
+                print(conditionMessage(e))
+                traceback()
+            })
+        }
+    }
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -191,6 +191,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new AppendNimble.Provider());
         SequencePipelineService.get().registerPipelineStep(new AppendTcr.Provider());
         SequencePipelineService.get().registerPipelineStep(new TcrFilter.Provider());
+        SequencePipelineService.get().registerPipelineStep(new PlotAssayFeatures.Provider());
 
         SequenceAnalysisService.get().registerFileHandler(new NimbleHandler());
     }

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

@@ -0,0 +1,49 @@
+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 PlotAssayFeatures extends AbstractCellMembraneStep
+{
+    public PlotAssayFeatures(PipelineContext ctx, PlotAssayFeatures.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("PlotAssayFeatures", "Plot Assay Features", "CellMembrane/Seurat", "This will create FeaturePlots for all features in the selected assays.", Arrays.asList(
+                    SeuratToolParameter.create("assayNames", "Assay Name(s)", "The name(s) of the asays to plot.", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("height", 150);
+                        put("delimiter", ",");
+                        put("allowBlank", false);
+                    }}, null).delimiter(",")
+            ), null, null);
+        }
+
+        @Override
+        public PlotAssayFeatures create(PipelineContext ctx)
+        {
+            return new PlotAssayFeatures(ctx, this);
+        }
+    }
+
+    @Override
+    public boolean createsSeuratObjects()
+    {
+        return false;
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "cite-plots";
+    }
+}