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Kyoko-wtnb / FUMA-circos-plot

Configs and descriptions of circos plots created on FUMA web application
MIT License
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Break axis in Manhattan plot region #1

Open bk11-lab opened 4 years ago

bk11-lab commented 4 years ago

Is it possible to break axis in the Manhattan plot region of circos plot in FUMA output so that we can see zoom in view of just GWAS significant locus? Help will be appreciated. Thanks.

Kyoko-wtnb commented 4 years ago

Hi @bhuwankhatri11 ,

I'm sorry for my slow response. Unfortunately, circos plot does not have a feature to break y axis, however you can manually add an additional layer of the plot. Here is a very brief instruction, let me know if you have any further questions.

First, you split SNPs in circos_snps.txt into two files based on the P-value where you want to break the axis, e.g. circos_snps1.txt and circos_snps2.txt in which circos_snps2.txt contains more significant SNPs.

Then add another layer of scatter plot in base.conf file. Within the first is the scatter plot of SNPs, so you want to add one more section, you can copy and paste, then change the file name to circos_snps1.txt and circos_snps2.txt. You also have to change r0 and r1 parameter. The default config has r0=1.1r and r1=1.45r for the SNPs scatter plot, the there is one more outer layer for the rsID which is r0=1.5r and r1=1.72r. You can either split two scatter plot between 1.1r and 1.45r or move rsID layer to further. For example, for circos_snps1.txt set r0=1.1r and r1=1.45r, for circos_snps2.txt set r0=1.5r and r1=1.75r then change rsID r0=1.8r and r1=1.95r, You will have to see how this looks like and refine the radius parameters.

Hope this helps.

Best, Kyoko