Highlighting significant loci

Cloufield / gwaslab

A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/

GNU General Public License v3.0

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Highlighting significant loci #71

Open soumickmj opened 7 months ago

soumickmj commented 7 months ago

Hi, Is it possible to Highlight the significant loci without specifying the rsIDs? It's currently like a 2 step process: -> plot to get the lead variants -> then, re-run the plot specifying the lead variants to highlight. Is it somehow possible to do it like a flag maybe? Thanks!

Cloufield commented 7 months ago

Hi, you can first simply run .get_lead(), which returns the sumstats of lead variants. (https://cloufield.github.io/gwaslab/ExtractLead/) And then pass the rsIDs of lead variants to plot_mqq highlight option. I will think about adding an option for this soon. Thanks for your feedback.

soumickmj commented 7 months ago

Lovely, thanks :)