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?