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# plot results
#
#usage: nohup R --vanilla < plotPfst --args plotHapOutput.txt
cmd_args <- commandArgs(trailingOnly = TRUE)
imageHap<-function(x){
pngName<-paste(c(x, format(Sys.time(), "%a%b%d_%H_%M_%S.pdf")), collapse="_")
dat<-read.table( x[1], header=FALSE )
pos<-dat[,1]
dat<-dat[,2:length(dat)]
print(head(dat))
hd<-dist(t(dat), method="binary")
or<-hclust(hd)
or$labels<-1:length(dat)
print(or$labels)
pdf(pngName, width=9, height=8)
par(mfrow=c(2,1))
image(1-as.matrix(dat[,or$order]), yaxt="n", xaxt="n", ylab="Haplotypes", xlab="SNP", cex.lab=1.1)
plot(or, main="", cex=1.1, lwd=2, sub="", xlab="")
dev.off()
}
imageHap(cmd_args)
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