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YinLiLin / CMplot

📊 Circular and Rectangular Manhattan Plot
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GWAS with different SNPs #2

Closed holtzy closed 6 years ago

holtzy commented 6 years ago

First of all, thanks for this nice package

I'm trying to output a stacked Manhattan plot with 3 GWAS summary statistics that have very few SNPs in common (CMplot function). It looks like only the SNPs that are common to the 3 dataset are plotted.

I am missing something? Or is it possible to improve the code to show all SNPs?

Thank you !

YinLiLin commented 6 years ago

Hi! holtzy,

Thanks very much for your using of CMplot! :rose: Actually, CMplot could only visualize the data that share the common SNPs with different p-values. If there is a NA for the SNP, it would be deleted whatever it has p-value for other traits. So i suggest that after merge the 3 GWAS results, you could try to replace NAs with value 1 for the non-common SNPs, then plot it with CMplot. Also i will update the codes to meet your problem. Hope it can solve your problem!

Thanks again!

Lilin

holtzy commented 6 years ago

Thanks for your answer and the hint! Yan