--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barplot.r	Sun Feb 10 18:31:51 2019 -0500
@@ -0,0 +1,48 @@
+if (length(commandArgs(TRUE)) == 0) {
+  system("Rscript barplot.r -h", intern = F)
+  q("no")
+}
+
+
+# load packages that are provided in the conda env
+options( show.error.messages=F,
+       error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+warnings()
+library(optparse)
+library(ggplot2)
+library(scales)
+
+
+
+#Arguments
+option_list = list(
+  make_option(
+    c("-i", "--input"),
+    default = NA,
+    type = 'character',
+    help = "Input file that contains count data (no header)"
+  ),
+  make_option(
+    c("-o", "--barplot"),
+    default = NA,
+    type = 'character',
+    help = "PDF output file"
+  )
+)
+
+opt = parse_args(OptionParser(option_list = option_list),
+                 args = commandArgs(trailingOnly = TRUE))
+
+
+## 
+annotations = read.delim(opt$input, header=F)
+colnames(annotations) = c("class", "counts")
+annotations = cbind(annotations, fraction=annotations$counts/annotations$counts[1])
+annotations = annotations[-1,]
+# ggplot2 plotting
+ggplot(annotations, aes(x="classes", y=fraction, fill=class)) +
+geom_bar(width = .7, position=position_stack(), stat = "identity") +
+geom_text(aes(label = percent(fraction)), position = position_stack(vjust = 0.5),size = 4)
+ggtitle('Class proportions') 
+ggsave(file=opt$barplot, device="pdf")