Support cellbender for CITE-seq and/or RNA

Author: bbimber

singlecell/resources/chunks/AppendCiteSeq.R

@@ -16,7 +16,7 @@ for (datasetId in names(seuratObjects)) {
     matrixDir <- featureData[[datasetId]]
     if (!is.null(matrixDir)) {
         tryCatch({
-            seuratObj <- CellMembrane::AppendCiteSeq(seuratObj, unfilteredMatrixDir = matrixDir, normalizeMethod = normalizeMethod, datasetId = datasetId, featureMetadata = featureMetadata, adtWhitelist = adtWhitelist)
+            seuratObj <- CellMembrane::AppendCiteSeq(seuratObj, unfilteredMatrixDir = matrixDir, normalizeMethod = normalizeMethod, datasetId = datasetId, featureMetadata = featureMetadata, adtWhitelist = adtWhitelist, runCellBender = runCellBender)
         }, error = function(e){
             print(paste0('Error running AppendCiteSeq for: ', datasetId))
             print(conditionMessage(e))

singlecell/resources/chunks/PrepareRawCounts.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     rawCountDir <- seuratObjects[[datasetId]]
 
     datasetName <- datasetIdToName[[datasetId]]
-    seuratObj <- CellMembrane::ReadAndFilter10xData(dataDir = rawCountDir, datasetId = datasetId, datasetName = datasetName, emptyDropsLower = emptyDropsLower, emptyDropsFdrThreshold = emptyDropsFdrThreshold, useEmptyDropsCellRanger = useEmptyDropsCellRanger, nExpectedCells = nExpectedCells)
+    seuratObj <- CellMembrane::ReadAndFilter10xData(dataDir = rawCountDir, datasetId = datasetId, datasetName = datasetName, emptyDropsLower = emptyDropsLower, emptyDropsFdrThreshold = emptyDropsFdrThreshold, useEmptyDropsCellRanger = useEmptyDropsCellRanger, nExpectedCells = nExpectedCells, useCellBender = useCellBender)
 
     if (!is.null(maxAllowableCells) && ncol(seuratObj) > maxAllowableCells) {
         addErrorMessage(paste0('The seurat object has ', ncol(seuratObj), ' cells, which is more than the max allowable cells (', maxAllowableCells, '). Please review emptyDrops results as this probably means thresholds were suboptimal.'))

singlecell/resources/web/singlecell/panel/SingleCellProcessingPanel.js

@@ -222,58 +222,7 @@ Ext4.define('SingleCell.panel.SingleCellProcessingPanel', {
                 singleTool: true,
                 comboValue: 'PrepareRawCounts',
                 sectionDescription: 'This section allows you to control the parsing of the raw 10x count data',
-                toolConfig: {
-                    singleCellRawData: [{
-                        description: 'Options related to processing the 10x matrix into a seurat object',
-                        label: 'Prepare Raw Counts',
-                        name: 'PrepareRawCounts',
-                        parameters: [{
-                            fieldXtype: 'ldk-integerfield',
-                            name: 'emptyDropsLower',
-                            label: 'EmptyDrops Lower',
-                            description: 'Passed to DropletUtils::emptyDrops lower argument',
-                            defaultValue: 200,
-                            additionalExtConfig: {
-                                minValue: 0
-                            }
-                        }, {
-                            fieldXtype: 'ldk-numberfield',
-                            name: 'emptyDropsFdrThreshold',
-                            label: 'EmptyDrops FDR Threshold',
-                            description: 'The FDR limit used to filter the results of DropletUtils::emptyDrops',
-                            defaultValue: 0.001,
-                            additionalExtConfig: {
-                                minValue: 0,
-                                decimalPrecision: 4
-                            }
-                        }, {
-                            fieldXtype: 'ldk-integerfield',
-                            name: 'maxAllowableCells',
-                            label: 'Max Cells Allowed',
-                            description: 'If more than this many cells are predicted by EmptyDrops, the job will fail',
-                            defaultValue: 20000,
-                            additionalExtConfig: {
-                                minValue: 0
-                            }
-                        }, {
-                            fieldXtype: 'checkbox',
-                            name: 'useEmptyDropsCellRanger',
-                            label: 'Use emptyDropsCellRanger',
-                            description: 'If checked, this will run emptyDropsCellRanger instead of emptyDrops',
-                            checked: false,
-                            inputValue: true
-                        }, {
-                            fieldXtype: 'ldk-integerfield',
-                            name: 'nExpectedCells',
-                            label: '# Expected Cells',
-                            description: 'Only applied if emptyDropsCellRanger is selected. Passed to n.expected.cells argument',
-                            defaultValue: 8000,
-                            additionalExtConfig: {
-                                minValue: 0
-                            }
-                        }]
-                    }]
-                }
+                toolConfig: results
             });
         }
 

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

@@ -146,8 +146,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new MergeSeurat.Provider());
         SequencePipelineService.get().registerPipelineStep(new NormalizeAndScale.Provider());
 
-        //Note: this should not be registered normally. It is used directly in ProcessSingleCellHandler
-        //SequencePipelineService.get().registerPipelineStep(new PrepareRawCounts.Provider());
+        SequencePipelineService.get().registerPipelineStep(new PrepareRawCounts.Provider());
 
         SequencePipelineService.get().registerPipelineStep(new RemoveCellCycle.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunCellHashing.Provider());

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

@@ -50,10 +50,14 @@ private static List<ToolParameterDescriptor> getParams()
     {
         List<ToolParameterDescriptor> ret = new ArrayList<>();
         ret.add(SeuratToolParameter.create("normalizeMethod", "Normalization Method", "", "ldk-simplecombo", new JSONObject(){{
-            put("storeValues", "dsb");
+            put("storeValues", "dsb;clr");
             put("initialValues", "dsb");
         }}, "dsb"));
 
+        ret.add(SeuratToolParameter.create("runCellBender", "Run CellBender", "If checked, cellbender will be run on the raw count matrix to remove background/ambient RNA signal", "checkbox", new JSONObject(){{
+
+        }}, false));
+
         return ret;
     }
 

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

@@ -1,6 +1,7 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
 import org.apache.logging.log4j.Logger;
+import org.json.JSONObject;
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.pipeline.PipelineJob;
@@ -33,7 +34,10 @@ public Provider()
                     SeuratToolParameter.create("emptyDropsFdrThreshold", "FDR Threshold", "The FDR limit used to filter the results of DropletUtils::emptyDrops", "ldk-numberfield", null, 0.001),
                     SeuratToolParameter.create("maxAllowableCells", "Max Cells Allowed", "If more than this many cells are predicted by EmptyDrops, the job will fail", "ldk-integerfield", null, 20000),
                     SeuratToolParameter.create("useEmptyDropsCellRanger", "Use emptyDropsCellRanger", "If checked, this will run emptyDropsCellRanger instead of emptyDrops", "checkbox", null, false),
-                    SeuratToolParameter.create("nExpectedCells", "# Expected Cells", "Only applied if emptyDropsCellRanger is selected. Passed to n.expected.cells argument", "ldk-integerfield", null, false)
+                    SeuratToolParameter.create("nExpectedCells", "# Expected Cells", "Only applied if emptyDropsCellRanger is selected. Passed to n.expected.cells argument", "ldk-integerfield", null, false),
+                    SeuratToolParameter.create("runCellBender", "Run CellBender", "If checked, cellbender will be run on the raw count matrix (instead of emptyDrops) to remove background/ambient RNA signal", "checkbox", new JSONObject(){{
+
+                    }}, false)
             ), null, null);
         }