locuszoomplot

Pure Python plotting of genomic regions around a variant

This is a python module that provides python plotting functions for the R2 and p-values of variants in a nearby region of a reference or target variant.

Here's a basic plot:

The example code is at examples/plot_basic_locuszoom.py

Dependencies

The implementation relies on

• databases from locuszoom-1.4 at https://statgen.sph.umich.edu/locuszoom/download/locuszoom_1.4.tgz
• SQLite
• plink 1.90 at https://www.cog-genomics.org/plink/1.9/

Issues

Sometimes if a gene region overlaps the window edges there's some displacement of the gene name in the plot