Separate CITE-seq dist() and PCA reduction steps

Author: bbimber

singlecell/resources/chunks/CiteSeqDimRedux.R

@@ -2,8 +2,18 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- seuratObjects[[datasetId]]
     seuratObjects[[datasetId]] <- NULL
 
-    #TODO: what if not used?
-    seuratObj <- bindArgs(CellMembrane::CiteSeqDimRedux, seuratObj)()
+    if (!(assayName %in% names(seuratObj@assays))) {
+        print('ADT assay not present, skipping')
+    } else {
+        tryCatch({
+            seuratObj <- bindArgs(CellMembrane::CiteSeqDimRedux, seuratObj)()
+        }, error = function(e){
+            conditionMessage(e)
+            print(paste0('Error running CiteSeqDimRedux'))
+            print(conditionMessage(e))
+            traceback()
+        })
+    }
 
     newSeuratObjects[[datasetId]] <- seuratObj
 

singlecell/resources/chunks/CiteSeqPca.R

@@ -0,0 +1,16 @@
+for (datasetId in names(seuratObjects)) {
+    seuratObj <- seuratObjects[[datasetId]]
+    seuratObjects[[datasetId]] <- NULL
+
+    if (!(assayName %in% names(seuratObj@assays))) {
+        print('ADT assay not present, skipping')
+    } else {
+        seuratObj <- bindArgs(CellMembrane::RunAdtPca, seuratObj)()
+    }
+
+    newSeuratObjects[[datasetId]] <- seuratObj
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

singlecell/resources/chunks/CiteSeqWnn.R

@@ -2,7 +2,11 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- seuratObjects[[datasetId]]
     seuratObjects[[datasetId]] <- NULL
 
-    seuratObj <- CellMembrane::RunSeuratWnn(seuratObj)
+    if (!(assayName %in% names(seuratObj@assays))) {
+        print('ADT assay not present, skipping')
+    } else {
+        seuratObj <- bindArgs(CellMembrane::RunSeuratWnn, seuratObj)()
+    }
 
     newSeuratObjects[[datasetId]] <- seuratObj
 

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

@@ -38,7 +38,9 @@
 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.CiteSeqPca;
 import org.labkey.singlecell.pipeline.singlecell.CiteSeqWnn;
+import org.labkey.singlecell.pipeline.singlecell.DimPlots;
 import org.labkey.singlecell.pipeline.singlecell.DoubletFinder;
 import org.labkey.singlecell.pipeline.singlecell.Downsample;
 import org.labkey.singlecell.pipeline.singlecell.FilterRawCounts;
@@ -169,6 +171,8 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new CiteSeqDimRedux.Provider());
         SequencePipelineService.get().registerPipelineStep(new CiteSeqWnn.Provider());
         SequencePipelineService.get().registerPipelineStep(new AvgExpression.Provider());
+        SequencePipelineService.get().registerPipelineStep(new DimPlots.Provider());
+        SequencePipelineService.get().registerPipelineStep(new CiteSeqPca.Provider());
     }
 
     @Override

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

@@ -19,7 +19,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("CiteSeqDimRedux", "CiteSeq DimRedux", "CellMembrane/Seurat", "This will run DimRedux steps on the ADT data.", Arrays.asList(
+            super("CiteSeqDimRedux", "CiteSeq DimRedux (distance)", "CellMembrane/Seurat", "This will run DimRedux steps on the ADT data.", Arrays.asList(
                     SeuratToolParameter.create("performClrNormalization", "Perform CLR Normalization", "If true, Seurat CLR normalization will be performed. Otherwise any pre-existing normalization is used.", "checkbox", new JSONObject(){{
                         put("checked", true);
                     }}, true, "performClrNormalization", true)

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

@@ -0,0 +1,41 @@
+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 CiteSeqPca extends AbstractCellMembraneStep
+{
+    public CiteSeqPca(PipelineContext ctx, CiteSeqPca.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("CiteSeqPca", "CiteSeq/ADT PCA", "CellMembrane/Seurat", "This will run PCA on the ADT data.", Arrays.asList(
+                    SeuratToolParameter.create("performClrNormalization", "Perform CLR Normalization", "If true, Seurat CLR normalization will be performed. Otherwise any pre-existing normalization is used.", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true, "performClrNormalization", true)
+            ), null, null);
+        }
+
+        @Override
+        public CiteSeqPca create(PipelineContext ctx)
+        {
+            return new CiteSeqPca(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "cite-pca";
+    }
+}