#!/usr/bin/Rscript
scaleValues<-1
title<-""
args <- commandArgs(trailingOnly = TRUE)
if(length(args)>1){
   	inputFile<-args[1]
   	outFile<-args[2]
} else {
  	cat("Usage: ./correlationPlot.R <InputData> <OutputFile.eps> <SCALING> <TITLE>\n");
  	cat("  <InputData>: Tab separated file of values with column names  REQUIRED\n");
  	cat("  <OutputFile.eps>: Output eps file  REQUIRED\n");
  	cat("  <SCALING>: Scale correlation values (default 1) set 0 to deactivate OPTIONAL\n");
  	cat("  <TITLE>: Title of the plot OPTIONAL\n");
	q()
}

if(length(args)>2){
	scaleValues<-args[3]
}

if(length(args)>3){
	title<-args[4]
}

panel.hist <- function(x, ...)
{
  usr <- par("usr"); on.exit(par(usr))
  par(usr = c(usr[1:2], 0, 1.5) )
  h <- hist(x, plot = FALSE)
  breaks <- h$breaks; nB <- length(breaks)
  y <- h$counts; y <- y/max(y)
  rect(breaks[-nB], 0, breaks[-1], y, col="cyan", ...)
}



if(scaleValues!=0){

	panel.cor <- function(x, y, digits=2, prefix="", cex.cor, ...)
	{
		usr <- par("usr"); on.exit(par(usr))
		par(usr = c(0, 1, 0, 1))
		r <- cor(x, y)
		txt <- formatC(c(r, 0.0123456789), digits=digits, format="f")[1]
		txt <- paste(prefix, txt, sep="")

		absr<- abs(cor(x, y))
		abstxt<- formatC(c(absr, 0.0123456789), digits=digits, format="f")[1]
		abstxt <- paste(prefix, abstxt, sep="")

		if(missing(cex.cor)) cex.cor <- 0.8/strwidth(abstxt)
		text(0.5, 0.5, txt, cex = cex.cor * absr)
	}
} else {
	panel.cor <- function(x, y, digits=2, prefix="", cex.cor, ...) 
	{
		usr <- par("usr"); on.exit(par(usr))
		par(usr = c(0, 1, 0, 1))
		r <- cor(x, y)
		txt <- formatC(c(r, 0.0123456789), digits=digits, format="f")[1]
		txt <- paste(prefix, txt, sep="")

		absr<- abs(cor(x, y))
		abstxt<- formatC(c(absr, 0.0123456789), digits=digits, format="f")[1]
		abstxt <- paste(prefix, abstxt, sep="")
		if(missing(cex.cor)) cex.cor <- 0.8/strwidth(abstxt)
		text(0.5, 0.5, txt, cex = cex.cor * 0.8 )
	}
}

data<-read.table(inputFile, sep="\t",header=T)
setEPS()
postscript(outFile)
#pairs(data, lower.panel=panel.smooth, upper.panel=panel.cor,pch='.',  main=title) 
names(data) <- c("Unif MS1", "Unif MS2", "Entropy", "MFE CO", "Rfam CO", "Native Cont")
pairs(data, lower.panel=panel.smooth, upper.panel=panel.cor,diag.panel=panel.hist,pch='.',  main=title) 
dev.off()