Plotting Cnv Association And Gwas Association In A Single Plot

Question

[Ryan D]

I'm familiar with some ways to make Manhattan plots, the easiest and most flexible I've found is Stephen Turner's qqman, from Getting Genetics Done, located here.

Manhattans are useful for showing P-values for individual SNPs, but is there a simple way to include other types of genetic architecture in such a plot? Specifically I am interested in plotting (as bars or in a different color) CNVs that may overlap these SNPs and span 10s to 100s of kb. Best way to do this? Any programs that permit p-values for more than SNPs and yet permit a Manhattan-esque (that is genome-wide) presentation of results?

Answer 1

[brentp]

I have a script that generates manhattan plots here.

The code is quite simple and I think it would be easy to add bars. You can just find the ax object in the code and use ax.axhspan() or ax.add_patch(plt.Rectangle()) to show the CNV's.

[Ryan D]

Thanks. But I'm getting some error when I try to execute it.

[rx@brie ~] python manhattan-plot.py --cols 0,1,2 delete.txt File "manhattan-plot.py", line 26 achr = a[3:] if a.startswith("chr") else a ^ SyntaxError: invalid syntax

Any ideas?

[brentp]

Yes, use python2.7. :) or change it to if a.startswith("chr"): achr = a[3:] n else: achr = a

[CHANG]

I have a file with chr, start, end, log2ratio from segmented tumor/normal copy number data. I notice you script takes in chr, position, and value only, do you suggest I take the midpoint between start and end of each segments as "position" ?

Answer 2

[Neilfws]

Since these plots are essentially just quantitative data (Y) versus chromosomal coordinates (X), I'm guessing you could cook something up using GenomeGraphs.

[Ryan D]

This looks like it might be useful, though it's not immediately clear to me from the manual that this would excel in generating Manhattan style plots.