Allow use to specify clusterResolutions

Author: bbimber

singlecell/resources/chunks/FindClustersAndDimRedux.R

@@ -19,7 +19,21 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- CellMembrane::FindClustersAndDimRedux(seuratObj, minDimsToUse = minDimsToUse, useLeiden = useLeiden)
+    if (all(is.null(clusterResolutions))) {
+        clusterResolutions <- c(0.2, 0.4, 0.6, 0.8, 1.2)
+    } else if (is.character(clusterResolutions)) {
+        clusterResolutionsOrig <- clusterResolutions
+        clusterResolutions <- gsub(clusterResolutions, pattern = ' ', replacement = '')
+        clusterResolutions <- unlist(strsplit(clusterResolutions, split = ','))
+        clusterResolutions <- as.numeric(clusterResolutions)
+        if (any(is.na(clusterResolutions))) {
+            stop(paste0('Some values for clusterResolutions were not numeric: ', clusterResolutionsOrig))
+        }
+    } else {
+        stop('Must provide a value for clusterResolutions')
+    }
+
+    seuratObj <- CellMembrane::FindClustersAndDimRedux(seuratObj, minDimsToUse = minDimsToUse, useLeiden = useLeiden, clusterResolutions = clusterResolutions)
 
     saveData(seuratObj, datasetId)
 

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

@@ -27,8 +27,9 @@ public Provider()
                     }}, 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);
+                    }}, false),
+                    SeuratToolParameter.create("clusterResolutions", "Cluster Resolutions", "A comma-separated list of resolution. If blank, it will default to 0.2, 0.4, 0.6, 0.8, 1.2", "textfield", null, null)
+                    ), null, "0.2,0.4,0.6,0.8,1.2");
         }