--- a/coverage_plotting.R	Fri Oct 18 19:18:50 2019 -0400
+++ b/coverage_plotting.R	Sun May 09 17:10:07 2021 +0000
@@ -1,53 +1,56 @@
 #!/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_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)
+hlp <- paste(hlp_description, hlp_usage, hlp_dataframe, hlp_type, hlp_output, sep = "\n")
 
 # Setup R error handling to go to stderr
-options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+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")
+    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)
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
+args <- parse_args(parser)
 
-if ( !('dataframe' %in% names(args)) || !('output' %in% names(args))) {
+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")
+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")
+    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$output, paper="special", height=11.69, width=8.2677)
+pdf(file = args$output, paper = "special", height = 11.69, width = 8.2677)
 plot(graph, newpage = T)
 dev.off()