Bugfix to FindClustersAndDimRedux

Author: bbimber

singlecell/resources/chunks/FindClustersAndDimRedux.R

@@ -15,24 +15,26 @@ if (!reticulate::py_module_available(module = 'leidenalg')) {
     }
 }
 
+if (all(is.null(clusterResolutions)) || 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 if (is.numeric(clusterResolutions)) {
+    # No action needed
+} else {
+    stop('Must provide a value for clusterResolutions')
+}
+
 for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-    if (all(is.null(clusterResolutions)) || 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)