diff phyloseq_plot_bar.R @ 5:1003ce695d6a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq commit 53ece29ec3f7e3c2c51d0ff9849e6193863cca71

--- a/phyloseq_plot_bar.R	Fri Jan 10 14:57:37 2025 +0000
+++ b/phyloseq_plot_bar.R	Sat Jan 25 17:08:17 2025 +0000
@@ -127,9 +127,11 @@
 
 # Generate bar plot
 if (!is.null(opt$x) && opt$x != "") {
-    p <- plot_bar(physeq, x = opt$x, fill = opt$fill)
+    p <- plot_bar(physeq, x = opt$x, fill = opt$fill) +
+        geom_bar(aes(color = NULL, fill = !!sym(opt$fill)), stat = "identity", position = "stack")
 } else {
-    p <- plot_bar(physeq, fill = opt$fill) # If no x is provided, don't include x
+    p <- plot_bar(physeq, fill = opt$fill) +
+        geom_bar(aes(color = NULL, fill = !!sym(opt$fill)), stat = "identity", position = "stack")
 }
 
 # Only facet if the facet variable is provided and exists in the sample data
@@ -141,6 +143,7 @@
     }
 }
 
+
 # Save to output file
 ggsave(
     filename = opt$output,