plotSmoothed.R

# Smooth plot of wcFst, pFst or abba-baba
#
#usage:  nohup R --vanilla < plotPfst --args smoothedpFst.txt wcFst|pFst|abba-baba

cmd_args <- commandArgs(trailingOnly = TRUE)

plotPfst<-function(x){
	require("ggplot2")
	dat<-read.table( x[1], header=FALSE )
	dat$V2<-1:length(dat$V2)
	pngName<-paste(c(x, format(Sys.time(), "%a%b%d_%H_%M_%S.png")), collapse="_")

	theplot<-NULL

	if(x[2] == "pFst"){
		theplot<-ggplot(dat, aes(x=V2, y=-log10(V5), colour=V4))+geom_point()+theme_grey(15)+labs(x="SNP index", y="-log10(smoothed pFst)")+scale_colour_continuous(low="grey", high="red", name="variants in window")
	}
	if(x[2] == "wcFst"){
		theplot<-ggplot(dat, aes(x=V2, y=V5, colour=V4))+geom_point()+theme_grey(15)+labs(x="SNP index", y="smoothed wcFst")+scale_colour_continuous(low="grey", high="red", name="variants in window")
	}
	if(x[2] == "xpEHH"){
		theplot<-ggplot(dat, aes(x=V2, y=V5, colour=V4))+geom_point()+theme_grey(15)+labs(x="SNP index", y="smoothed xpEHH")+scale_colour_continuous(low="grey", high="red", name="variants in window")
	}
	if(x[2] == "abba-baba"){
		theplot<-ggplot(dat, aes(x=V3, y=V5, colour=V4))+geom_point()+theme_grey(15)+labs(x="SNP index", y="D-statistic")+scale_colour_continuous(low="grey", high="red", name="variants in window")
	}
	ggsave(filename=pngName, width=20, height=4, units="in", theplot)
}

plotPfst(cmd_args)