Support additional emptyDrops options

Author: bbimber

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)
+    seuratObj <- CellMembrane::ReadAndFilter10xData(dataDir = rawCountDir, datasetId = datasetId, datasetName = datasetName, emptyDropsLower = emptyDropsLower, emptyDropsFdrThreshold = emptyDropsFdrThreshold, useEmptyDropsCellRanger = useEmptyDropsCellRanger, nExpectedCells = nExpectedCells)
 
     if (!is.null(maxAllowableCells) && ncol(seuratObj) > maxAllowableCells) {
         stop(paste0('The seurat object has more than the max allowable cells. Please review emptyDrops results'))

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

@@ -200,35 +200,6 @@ Ext4.define('SingleCell.panel.SingleCellProcessingPanel', {
     },
 
     onDataLoad: function(results){
-        results.prepareRawData = [{
-            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,
-                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,
-                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,
-                minValue: 0
-            }]
-        }];
-
         this.add([this.getFilePanelCfg(), this.getProtocolPanelCfg(),{
             xtype: 'panel',
             title: 'Analysis Options',
@@ -247,10 +218,53 @@ Ext4.define('SingleCell.panel.SingleCellProcessingPanel', {
             items.push({
                 xtype: 'sequenceanalysis-analysissectionpanel',
                 title: 'Prepare Raw Data',
-                stepType: 'prepareRawData',
+                stepType: 'singleCell',
                 singleTool: true,
+                comboValue: 'prepareRawData',
                 sectionDescription: 'This section allows you to control the parsing of the raw 10x count data',
-                toolConfig: results
+                toolConfig: {
+                    prepareRawData: [{
+                        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,
+                            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,
+                            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,
+                            minValue: 0
+                        }, {
+                            fieldXtype: 'checkbox',
+                            name: 'useEmptyDropsCellRanger',
+                            label: 'Use emptyDropsCellRanger',
+                            description: 'If checked, this will run emptyDropsCellRanger instead of emptyDrops',
+                            checked: false,
+                            inputValue: true
+                        }, {
+                            fieldXtype: 'checkbox',
+                            name: 'nExpectedCells',
+                            label: '# Expected Cells',
+                            description: 'Only applied if emptyDropsCellRanger is selected. Passed to n.expected.cells argument',
+                            value: 8000
+                        }]
+                    }]
+                }
             });
         }
 

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

@@ -26,7 +26,9 @@ public Provider()
             super("PrepareRawCounts", LABEL, "CellMembrane/Seurat", "This step reads the raw count matrix/matrices, and runs EmptyDrops to provide an unfiltered count matrix.", Arrays.asList(
                     SeuratToolParameter.create("emptyDropsLower", "Lower", "Passed to DropletUtils::emptyDrops lower argument", "ldk-integerfield", null, 200),
                     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("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)
             ), null, null);
         }