Plotting Cnv Association And Gwas Association In A Single Plot

Question: Plotting Cnv Association And Gwas Association In A Single Plot

7.9 years ago by

Ryan D • 3.3k

USA

Ryan D • 3.3k wrote:

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?

gwas visualization cnv • 3.7k views

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modified 3.8 years ago by Biostar ♦♦ 20 • written 7.9 years ago by Ryan D • 3.3k

7.9 years ago by

brentp ♦ 23k

Salt Lake City, UT

brentp ♦ 23k wrote:

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.

ADD COMMENT • link written 7.9 years ago by brentp ♦ 23k

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?

ADD REPLY • link written 7.9 years ago by Ryan D • 3.3k

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

ADD REPLY • link written 7.9 years ago by brentp ♦ 23k

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" ?

ADD REPLY • link written 4.8 years ago by CHANG • 40

7.9 years ago by

Neilfws ♦ 48k

Sydney, Australia

Neilfws ♦ 48k wrote:

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

ADD COMMENT • link written 7.9 years ago by Neilfws ♦ 48k

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.

ADD REPLY • link written 7.9 years ago by Ryan D • 3.3k

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