Support AvgExpression single cell step

Author: bbimber

singlecell/resources/chunks/AvgExpression.R

@@ -2,13 +2,9 @@ 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)
+    df <- CellMembrane::AvgExpression(seuratObj, groupField = groupField)
+    write.table(df, file = paste0(outputPrefix, '.', datasetId, '.avg.', groupField, '.txt'), sep = '\t', row.names = FALSE, quote = FALSE)
+    rm(df)
 
     # Cleanup
     rm(seuratObj)

singlecell/resources/chunks/DimPlots.R

@@ -0,0 +1,20 @@
+for (datasetId in names(seuratObjects)) {
+    seuratObj <- seuratObjects[[datasetId]]
+    seuratObjects[[datasetId]] <- NULL
+
+    for (field in fieldNames) {
+        if (!(field %in% names(seuratObj@meta.data))) {
+            next
+        }
+
+        P1 <- Seurat::DimPlot(seuratObj, group.by = field, reduction = 'tsne')
+        P2 <- Seurat::DimPlot(seuratObj, group.by = field, reduction = 'umap')
+
+        P1 <- P1 | P2
+        P1 <- P1 + patchwork::plot_annotation(title = field)
+    }
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -39,7 +39,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("AppendCiteSeq", "Possibly Append CITE-seq Data", "OOSAP", "If available, this will process and append CITE-seq data to the Seurat object(s).", getParams(), null, null);
+            super("AppendCiteSeq", "Possibly Append CITE-seq Data", "CellMembrane", "If available, this will process and append CITE-seq data to the Seurat object(s).", getParams(), null, null);
         }
 
         @Override

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

@@ -32,5 +32,11 @@ public AvgExpression create(PipelineContext ctx)
             return new AvgExpression(ctx, this);
         }
     }
+
+    @Override
+    public boolean createsSeuratObjects()
+    {
+        return false;
+    }
 }
 

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

@@ -17,7 +17,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("CiteSeqDimRedux", "CiteSeq DimRedux", "Seurat", "This will run DimRedux steps on the ADT data.", Arrays.asList(
+            super("CiteSeqDimRedux", "CiteSeq DimRedux", "CellMembrane/Seurat", "This will run DimRedux steps on the ADT data.", Arrays.asList(
 
             ), null, null);
         }

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

@@ -0,0 +1,52 @@
+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 DimPlots extends AbstractCellMembraneStep
+{
+    public DimPlots(PipelineContext ctx, DimPlots.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("DimPlots", "Create DimPlots", "Seurat", "This will generate DimPlots grouped by the 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 DimPlots create(PipelineContext ctx)
+        {
+            return new DimPlots(ctx, this);
+        }
+    }
+
+    @Override
+    public Collection<String> getRLibraries()
+    {
+        return PageFlowUtil.set("Seurat", "patchwork");
+    }
+
+    @Override
+    public boolean createsSeuratObjects()
+    {
+        return false;
+    }
+}

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

@@ -19,7 +19,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("Downsample", "Downsample Cells", "OOSAP", "This will downsample cells from the input object(s) based on the parameters below. Downsampling will be applied independently to each incoming Seurat object. If a second field is provided, cells within each object will be subset using that field, and then downsampled.", Arrays.asList(
+            super("Downsample", "Downsample Cells", "CellMembrane/Seurat", "This will downsample cells from the input object(s) based on the parameters below. Downsampling will be applied independently to each incoming Seurat object. If a second field is provided, cells within each object will be subset using that field, and then downsampled.", Arrays.asList(
                     SeuratToolParameter.create("targetCells", "Target Cells Per Unit of Data", "Each unit of data will be downsampled to this level", "ldk-integerfield", new JSONObject(){{
                         put("allowBlank", false);
                     }}, null),

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

@@ -19,7 +19,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("FilterRawCounts", "Filter Raw Counts", "Seurat/OOSAP", "This will use OOSAP/Seurat to perform basic filtering on cells based on UMI count, feature count, etc.", Arrays.asList(
+            super("FilterRawCounts", "Filter Raw Counts", "CellMembrane/Seurat", "This will use CellMembrane/Seurat to perform basic filtering on cells based on UMI count, feature count, etc.", Arrays.asList(
                     SeuratToolParameter.create("nCountRnaLow", "Min UMI Count", "Cells with UMI counts below this value will be discarded", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
                     }}, 0, "nCount_RNA.low", false),

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

@@ -19,7 +19,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("FindClustersAndDimRedux", "Find Clusters And Dim Redux", "OOSAP", "This will run tSNA and UMAP for the input object.", Arrays.asList(
+            super("FindClustersAndDimRedux", "Find Clusters And Dim Redux", "CellMembrane/Seurat", "This will run tSNA and UMAP for the input object.", Arrays.asList(
                     SeuratToolParameter.create("minDimsToUse", "Min. PCs to Use", "The minimum number of PCs to use", "ldk-integerfield", new JSONObject(){{
                         put("minValue", 0);
                     }}, 15)

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

@@ -19,7 +19,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("FindMarkers", "Find Markers", "OOSAP", "This will run Final_All_Markers on the input object(s), save the results as a TSV.", Arrays.asList(
+            super("FindMarkers", "Find Markers", "CellMembrane/Seurat", "This will run Final_All_Markers on the input object(s), save the results as a TSV.", Arrays.asList(
                     SeuratToolParameter.create("identFields", "Identity Field(s)", "When running FindMarkers, these field(s) will be used to group the data, identify markers for each group of cells. Enter one field per row.", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
                         put("allowBlank", false);
                         put("height", 200);