--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coverage_plotting.R	Mon Jul 24 06:27:50 2017 -0400
@@ -0,0 +1,53 @@
+#!/usr/bin/env Rscript
+
+# Help to be printed
+hlp_description = "This script takes a dataframe containing the coverage values for different miRNAs and plots them."
+hlp_usage = "Usage : coverage_ploting.R --dataframe [FILE] --type ['relative' or 'absolute'] --output [FILE]"
+hlp_dataframe = "--dataframe\tFILE\tThis is a dataframe containing coverage values obtained from mircounts.py"
+hlp_type = "--type\t\tSTRING\tType of ploting, either relative or absoute coverage values (default='relative')"
+hlp_output = "--output\tFILE\tFile to output the pdf to\n"
+
+hlp = paste(hlp_description,hlp_usage,hlp_dataframe,hlp_type,hlp_output,sep="\n")
+#print(hlp)
+
+# Setup R error handling to go to stderr
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+library(optparse)
+library(lattice)
+
+# Get arguments
+option_list <- list(
+    make_option(c("-d", "--dataframe"), type="character",
+                help="Dataframe containing coverage values obtained from mircounts.py"),
+    make_option(c("-t", "--type"), type="character", default="relative",
+                help="Type of plotting, either relative or absoute coverage values (default='relative')"),
+    make_option(c("-o", "--output"), type="character", help="File to output the pdf to")
+    )
+parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
+args = parse_args(parser)
+
+if ( !('dataframe' %in% names(args)) || !('output' %in% names(args))) {
+    stop("'--dataframe' and '--output' parametters are not optional. Please retry.")
+}
+
+# Plot
+coverage = read.delim(args$dataframe, header=T)
+if (args$type =="relative") {
+    graph = xyplot(Norm_count~Norm_offset | Mir_hairpin, data=coverage, col=c("darkblue"), type="l", lwd=1.5,
+                   scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5),
+                   strip=strip.custom(which.given=1, bg="lightblue"), layout=c(4,15),
+                   as.table=T, xlab="Normalized Counts", ylab="Normalized coordinates",
+                   main="miRNA coverage maps")
+} else {
+    graph = xyplot(Count~Offset | Mir_hairpin, data=coverage, col=c("darkblue"), type="l", lwd=1.5,
+                   scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5),
+                   strip=strip.custom(which.given=1, bg="lightblue"), layout=c(4,15),
+                   as.table=T, xlab="Counts", ylab="Coordinates",
+                   main="miRNA coverage plots")
+}
+
+# PDF output
+pdf(file=args$output, paper="special", height=11.69, width=8.2677)
+plot(graph, newpage = T)
+dev.off()