title: Good way to graph allele frequency of different SNPs along chromosomes
body: <p>I have a set of SNPs from different parts of the genome and their allele frequencies in various populations and metapopulations of interest. I want to plot the allele frequencies along the SNPs' genomic coordinates for all 22 autosomes.</p>
  <p>Basically, I want to generate something like this Figure 1A from Sankararaman et al. (2014) (<a href="http://www.nature.com/nature/journal/v507/n7492/fig_tab/nature12961_F1.html" rel="nofollow noreferrer">http://www.nature.com/nature/journal/v507/n7492/fig_tab/nature12961_F1.html</a>) except the Y-axis would be frequency, all populations would be on the same graph (not separated), and I would have colored points instead of spikes.</p>
  <p>My data is formatted as such (MAF = minor allele frequency, which is what I want to graph)</p>
  <pre><code>CHR    SNP        COORD   CLST   A1   A2    MAF    MAC  NCHROBS
  1   rs###  2####  Region  G    A   0.4   400     1000
  </code></pre>
  <p>(It goes through all the SNPs for on region, and then it does them for the next region, and so forth)</p>
  <p>Any suggestions on how to do this in R? Thanks!</p>