Prevent Rplots generation

workflow/bin/quality_control.R

@@ -401,15 +401,16 @@ umap_dir <- paste0(outdir, "umaps/")
 dir.create(umap_dir, recursive=TRUE)
 
 for (grp in groups) {
-  DimPlot(seu, group.by=grp)
-  ggsave(paste0(umap_dir, grp, ".png"))
+  p <- DimPlot(seu, group.by=grp)
+  ggsave(paste0(umap_dir, grp, ".png"), plot = p)
 }
 
 # Create clustree plot
-clustree(seu, prefix = "RNA_snn_res.")
+p <- clustree(seu, prefix = "RNA_snn_res.")
 ggsave(paste0(outdir, "clustree.png"),
        height=12,
-       width=12*0.618)
+       width=12*0.618,
+       plot = p)
 
 # Create stress and double score plots
 p.list$doublet_score <- FeaturePlot(seu, "scDblFinder.score")