qmplot 0.0.1

qmplot: Create high-quality manhattan and QQ plots for PLINK association output (or any dataframe with chromosome, position, and p-value).

qmplot is a handy tool and Python package for creating high-quality manhattan and Q-Q plots from PLINK association output or any dataframe with chromosome, position and p-value.

This library is inspired by r-qqman.

Dependencies

qmplot supports Python 3.6+ and no longer supports Python 2.

Instatllation requires numpy, scipy, pandas and matplotlib.

Installation

qmplot is written by Python and release in PyPI. The latest stable release can be installed by running the following command:

pip install qmplot

Quick Start

We use a PLINK2.x association output data “gwas_plink_result.tsv” which is in tests/data directory, as the input for the plots below. Here is the format preview of “gwas_plink_result.tsv”:

#CHROM	POS	ID	REF	ALT	A1	TEST	OBS_CT	BETA	SE	T_STAT	P
1	904165	1_904165	G	A	A	ADD	282	-0.0908897	0.195476	-0.464967	0.642344
1	1563691	1_1563691	T	G	G	ADD	271	0.447021	0.422194	1.0588	0.290715
1	1707740	1_1707740	T	G	G	ADD	283	0.149911	0.161387	0.928888	0.353805
1	2284195	1_2284195	T	C	C	ADD	275	-0.024704	0.13966	-0.176887	0.859739
1	2779043	1_2779043	T	C	T	ADD	272	-0.111771	0.139929	-0.79877	0.425182
1	2944527	1_2944527	G	A	A	ADD	276	-0.054472	0.166038	-0.32807	0.743129
1	3803755	1_3803755	T	C	T	ADD	283	-0.0392713	0.128528	-0.305547	0.760193
1	4121584	1_4121584	A	G	G	ADD	279	0.120902	0.127063	0.951511	0.342239
1	4170048	1_4170048	C	T	T	ADD	280	0.250807	0.143423	1.74873	0.0815274

qmplot apply two ways to generate manhattan and Q-Q plots: