data <- read.table("asyncTable.norm.log2.txt", sep="\t", header=TRUE, row.names=1)

numPlots <- 29
ht <- ceiling(numPlots/5)*3;
pdf(file="compareAsynReps.pdf",width=15,height=ht,pointsize=10)
par(mfrow=c(7,5), cex.lab=1.5, col="darkblue", cex.axis=1.2, mar=c(5.01, 4.5, 4.01, 1.5))
names=colnames(data)

#loop through G1E
for (i in 1:6) {
   s=i+1
   if (s < 6) {
   for (k in s:6) {
   cr <- cor(data[,i], data[,k], method="spearman")
   p <- sprintf("rho %.2f", cr)
   plot(data[,i], data[,k], xlab=names[i], ylab=names[k], pch=18)
   abline(a=0, b=1, col="red")
   mtext(p,1,adj=1,line=3)
   }
   }
}

#loop through ER4
for (m in 7:12) {
   s=m+1
   if (s < 12) {
   for (n in s:12) {
   cr <- cor(data[,m], data[,n], method="spearman")
   p <- sprintf("rho %.2f", cr)
   plot(data[,m], data[,n], xlab=names[m], ylab=names[n], pch=18)
   abline(a=0, b=1, col="red")
   mtext(p,1,adj=1,line=3)
   }
   }
}

cr <- cor(data[,6], data[,12], method="spearman")
p <- sprintf("rho %.2f", cr)
plot(data[,6], data[,12], xlab=names[6], ylab=names[12], pch=18)
abline(a=0, b=1, col="red")
mtext(p,1,adj=1,line=3)

dev.off()