Metadata-Version: 1.2
Name: qmplot
Version: 0.0.1
Summary: qmplot: Create high-quality manhattan and QQ plots for PLINK association output (or any dataframe with chromosome, position, and p-value).
Home-page: https://github.com/ShujiaHuang/qmplot
Author: Shujia Huang
Author-email: huangshujia9@gmail.com
Maintainer: Shujia Huang
Maintainer-email: huangshujia9@gmail.com
License: BSD (3-clause)
Download-URL: https://github.com/ShujiaHuang/qmplot
Description: qmplot: A Python tool for creating high-quality manhattan and Q-Q plots from GWAS results.
        ==========================================================================================
        
        **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 <https://github.com/stephenturner/qqman>`__.
        
        Dependencies
        ------------
        
        qmplot supports Python 3.6+ and no longer supports Python 2.
        
        Instatllation requires `numpy <https://numpy.org/>`__,
        `scipy <https://www.scipy.org/>`__,
        `pandas <https://pandas.pydata.org/>`__ and
        `matplotlib <https://matplotlib.org/>`__.
        
        Installation
        ------------
        
        **qmplot** is written by Python and release in PyPI. The latest stable
        release can be installed by running the following command:
        
        .. code:: bash
        
                
                pip install qmplot
        
        Quick Start
        -----------
        
        We use a PLINK2.x association output data
        "`gwas_plink_result.tsv <tests/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:
        
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.7
Classifier: License :: OSI Approved :: BSD License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: POSIX
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS
