Add support for useLeiden

Author: bbimber

singlecell/resources/chunks/FindClustersAndDimRedux.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- CellMembrane::FindClustersAndDimRedux(seuratObj, minDimsToUse = minDimsToUse)
+    seuratObj <- CellMembrane::FindClustersAndDimRedux(seuratObj, minDimsToUse = minDimsToUse, useLeiden = useLeiden)
 
     saveData(seuratObj, datasetId)
 

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

@@ -24,8 +24,10 @@ public Provider()
                     SeuratToolParameter.create("minDimsToUse", "Min. PCs to Use", "The minimum number of PCs to use", "ldk-integerfield", new JSONObject()
                     {{
                         put("minValue", 0);
-                    }}, 15)
+                    }}, 15),
+                    SeuratToolParameter.create("useLeiden", "Use Leiden Clustering", "If true, FindClusters() will use algorith=4 (leiden), as opposed to the default (louvain)", "checkbox", new JSONObject(){{
 
+                    }}, false)
             ), null, null);
         }