Support additional parameter for split seurat

Author: bbimber

singlecell/resources/chunks/RunRiraClassification.R

@@ -2,8 +2,8 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- RIRA::RunCellTypist(seuratObj, modelName = 'RIRA_Immune_v1', maxBatchSize = maxBatchSize, columnPrefix = 'RIRA_Immune_v1.', retainProbabilityMatrix = retainProbabilityMatrix)
-    seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix, columnPrefix = 'RIRA_TNK_v2.')
+    seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
+    seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
 
     seuratObj$RIRA_TNK_v2.predicted_labels[seuratObj$RIRA_Immune_v1.majority_voting != 'T_NK'] <- 'Other'
 

singlecell/resources/chunks/SplitSeurat.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    newList <- CellMembrane::SplitSeurat(seuratObj, splitField = splitField, minCellsToKeep = minCellsToKeep)
+    newList <- CellMembrane::SplitSeurat(seuratObj, splitField = splitField, minCellsToKeep = minCellsToKeep, excludedClasses = excludedClasses)
     for (name in names(newList)) {
         saveData(newList[[name]], paste0(datasetId, '-', name))
     }

singlecell/resources/views/singleCellDataManagement.html

@@ -61,10 +61,27 @@
                         })
                     },{
                         name: 'Readsets Not Archived to SRA',
-                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'sequence_readsets', 'query.totalForwardReads~isnonblank': null, 'query.isArchived~eq': 0})
-                    },{
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
+                            schemaName: 'sequenceanalysis',
+                            queryName: 'sequence_readsets',
+                            'query.totalForwardReads~isnonblank': null,
+                            'query.isArchived~eq': 0}
+                        )
+                    }, {
                         name: 'Analyses Using Old Readsets',
-                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'sequence_analyses', 'query.readset/status~isnonblank': null})
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
+                            schemaName: 'sequenceanalysis',
+                            queryName: 'sequence_analyses',
+                            'query.readset/status~isnonblank': null
+                        })
+                    },{
+                        name: 'Orphan 10x Run Summaries',
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
+                            schemaName: 'sequenceanalysis',
+                            queryName: 'outputfiles',
+                            'query.category~eq': '10x Run Summary',
+                            'query.readset/totalOutputs~eq': 1
+                        })
                     }]
                 }]
             }]

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

@@ -26,7 +26,12 @@ public Provider()
                     SeuratToolParameter.create("minCellsToKeep", "Min Cells To Keep", "If provided, any subset with fewer than this many cells will be discarded. Use zero to keep all. Note: if the value is less than 1 it will be interpreted as a fraction of the total input cells", "ldk-numberfield", new JSONObject(){{
                         put("allowBlank", false);
                         put("decimalPrecision", 3);
-                    }}, 0.05)
+                    }}, 0.05),
+                    SeuratToolParameter.create("excludedClasses", "Excluded Classes", "A list, one per line, of any classes to be excluded from the split. Cells with these values we will placed into the Other subset", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("height", 150);
+                        put("delimiter", ",");
+                        put("stripCharsRe", "/(^['\"]+)|(['\"]+$)/g");
+                    }}, null, null, true).delimiter(",")
             ), null, null);
         }