# polygon eqtl + genes plots

#setwd("/Users/nanettecoetzer/Documents/Bioinformatics/MAIZE_project/eQTL_pipeline/April_2012_pipeline_scripts/July_2012")
data <- read.table("sliding_frequency.txt",sep="\t",header=TRUE)
num.chr = max(data[,2])


pdf(paste("Rplot_eQTL_genes_polygon.pdf",sep=""),width=20,height=12)
if (num.chr <= 6) {
	par(mfrow=c(2,3))
	}
if (num.chr>6 & num.chr<=9) {
	par(mfrow=c(3,3))
	}
if (num.chr>9 & num.chr<=12) {
	par(mfrow=c(3,4))
	}
if (num.chr>12 & num.chr<=15) {
	par(mfrow=c(3,5))
	}
if (num.chr>15 & num.chr<=20) {
	par(mfrow=c(4,5))
	}
	
len_trans <- length(data[,6])
max_trans <- sort(data[,6])[len_trans-3]

for (k in 1:num.chr) {
	bin1 <- data[data[,2]==k,1]
	bin <- c(1:length(bin1))
	cis <- data[data[,2]==k,5]
	trans <- data[data[,2]==k,6]
	genes <- data[data[,2]==k,7]
	m = max(trans)
	
	plot(bin,trans, ylim=c(0, max_trans), type="n",col="red", lwd=1, ylab="Frequency",main=paste("Chr ",k),xlab="Sliding window bins")
	polygon(c(0,genes,0),col="green",border="green")
	polygon(c(0,trans,0),col="red",border="red")
	polygon(c(0,cis,0),col="blue",border="blue")
	x <- 2.2*(max(bin)/3)
	legend(x,max_trans,c("genes","trans","cis"),col=c("green","red","blue"),lty=1,lwd=2)
	}
dev.off()