make sure has_celltypes is in supplemental

AlexsLemonade · Apr 25, 2024 · 2d3d30f · 2d3d30f
1 parent 1ff240c
commit 2d3d30f
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/templates/qc_report/celltypes_supplemental_report.rmd b/templates/qc_report/celltypes_supplemental_report.rmd
@@ -264,6 +264,9 @@ has_cellassign <- "cellassign" %in% metadata(processed_sce)$celltype_methods
 has_submitter <- "submitter" %in% metadata(processed_sce)$celltype_methods &&
   !all(is.na(processed_sce$submitter_celltype_annotation)) # make sure they aren't all NA
 
+# If at least 1 is present, we have cell type annotations.
+has_celltypes <- any(has_singler, has_cellassign, has_submitter)
+
 # check for umap and clusters
 has_umap <- "UMAP" %in% reducedDimNames(processed_sce)
 has_clusters <- "cluster" %in% names(colData(processed_sce))