Merge pull request #6986 from 10XGenomics/js/xenium_hotfix

fix(Xenium): load renamed feature
satijalab · Feb 28, 2023 · 6a8a1cd · 6a8a1cd
2 parents 9f6cc3f + e1620ee
commit 6a8a1cd
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/R/convenience.R b/R/convenience.R
@@ -201,7 +201,10 @@ LoadXenium <- function(data.dir, fov = 'fov', assay = 'Xenium') {
   )
 
   xenium.obj <- CreateSeuratObject(counts = data$matrix[["Gene Expression"]], assay = assay)
-  xenium.obj[["BlankCodeword"]] <- CreateAssayObject(counts = data$matrix[["Blank Codeword"]])
+  if("Blank Codeword" %in% names(data$matrix))
+    xenium.obj[["BlankCodeword"]] <- CreateAssayObject(counts = data$matrix[["Blank Codeword"]])
+  else
+    xenium.obj[["BlankCodeword"]] <- CreateAssayObject(counts = data$matrix[["Unassigned Codeword"]])
   xenium.obj[["ControlCodeword"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Codeword"]])
   xenium.obj[["ControlProbe"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Probe"]])