Add support for useLeiden

BimberLab · May 29, 2024 · 1549b62 · 1549b62
1 parent 85cca6d
commit 1549b62
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/singlecell/resources/chunks/FindClustersAndDimRedux.R b/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)
 

diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/FindClustersAndDimRedux.java b/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);
         }