Add more arguments for UCell scores

Author: bbimber

singlecell/resources/chunks/CalculateUCellScores.R

@@ -3,7 +3,7 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
     message(paste0('Loading dataset ', datasetId, ', with total cells: ', ncol(seuratObj)))
-    seuratObj <- RIRA::CalculateUCellScores(seuratObj)
+    seuratObj <- RIRA::CalculateUCellScores(seuratObj, storeRanks = storeRanks, assayName = assayName)
 
     saveData(seuratObj, datasetId)
 

singlecell/resources/chunks/CustomUCell.R

@@ -12,7 +12,7 @@ for (datasetId in names(seuratObjects)) {
     toCalculate[[vals[1]]] <- unlist(strsplit(vals[2], split = ','))
   }
 
-  seuratObj <- UCell::AddModuleScore_UCell(seuratObj, features = toCalculate)
+  seuratObj <- UCell::AddModuleScore_UCell(seuratObj, features = toCalculate, storeRanks = storeRanks, assay = assayName)
   saveData(seuratObj, datasetId)
 
   # Cleanup

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

@@ -1,7 +1,9 @@
 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;
 
@@ -19,7 +21,14 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("CalculateUCellScores", "Calculate UCell Scores", "Seurat", "This will generate UCell scores for a set of pre-defined gene modules", null, null, null);
+            super("CalculateUCellScores", "Calculate UCell Scores", "Seurat", "This will generate UCell scores for a set of pre-defined gene modules", Arrays.asList(
+                    SeuratToolParameter.create("storeRanks", "Store Ranks", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
+
+                    }}, false),
+                    SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
+
+                    }}, "RNA")
+            ), null, null);
         }
 
         @Override

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

@@ -4,12 +4,10 @@
 import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
 import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
+import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 
 import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Set;
 
 public class CustomUCell extends AbstractRiraStep
 {
@@ -31,7 +29,13 @@ public Provider()
                         put("height", 150);
                         put("width", 600);
                         put("delimiter", DELIM);
-                    }}, null)
+                    }}, null),
+                    SeuratToolParameter.create("storeRanks", "Store Ranks", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
+
+                    }}, false),
+                    SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "checkbox", new JSONObject(){{
+
+                    }}, "RNA")
             ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }