Good way to graph allele frequency of different SNPs along chromosomes

Question

[devenvyas]

I have allele frequencies for the Neanderthal allele at sites where both Neanderthal genomes are homozygous and overlap with putative introgressed haplotypes in the form of Plink frequency output (--freq --missing --within cluster --out output).

I want to plot the allele frequencies along the SNPs' genomic coordinates.

Basically, I want to generate something like this Figure 1A from Sankararaman et al. (2014) (http://www.nature.com/nature/journal/v507/n7492/fig_tab/nature12961_F1.html) except the Y-axis would be frequency.

Anyone know how I could do this?

Answer 1

[devenvyas]

I figured out how to modify Isran's code. In case anyone else needs/wants it, here it is.

snps<-read.table("filename.txt",header=T)

goodChrOrder <- c(1:22,"X","Y")
snps$CHR <- factor(snps$CHR,levels=goodChrOrder)

library(ggplot2)
freq = ggplot(snps,aes(COORD,MAF, colour=CLST)) + geom_point() +
  facet_wrap(~ CHR,ncol=2) + # separate plots for each chr, x-scales can differ from chr to chr
  ggtitle("Distribution of allele frequency across genome") +
  xlab("Position in the genome") + 
  ylab("SNP frequency") + 


pdf("filename.pdf",20,20)
print(freq)
dev.off()

Answer 2

[John]

I often use Irsan's solution from Plotting Density Of Snps On Chromosomes Works for me :)

[devenvyas]

Is there anyway to modify the code to display allele frequencies instead of density? Also, what about display frequencies in multiple populations?