Question: Plotting Cnv Association And Gwas Association In A Single Plot
2
gravatar for Ryan D
7.9 years ago by
Ryan D3.3k
USA
Ryan D3.3k 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
ADD COMMENTlink modified 3.8 years ago by Biostar ♦♦ 20 • written 7.9 years ago by Ryan D3.3k
3
gravatar for brentp
7.9 years ago by
brentp23k
Salt Lake City, UT
brentp23k 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 COMMENTlink written 7.9 years ago by brentp23k

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 REPLYlink written 7.9 years ago by Ryan D3.3k

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

ADD REPLYlink written 7.9 years ago by brentp23k

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 REPLYlink written 4.8 years ago by CHANG40
2
gravatar for Neilfws
7.9 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k 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 COMMENTlink written 7.9 years ago by Neilfws48k

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 REPLYlink written 7.9 years ago by Ryan D3.3k
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