Plot variants on the human mitochondrial genome.
Project description
mitoviz
Plot variants on the human mitochondrial genome.
Free software: MIT license
Documentation: https://mitoviz.readthedocs.io
GitHub repo: https://github.com/robertopreste/mitoviz
Features
mitoviz is a simple python package to plot human mitochondrial variants on a graphical representation of the human mitochondrial genome. It currently supports plotting variants stored in a VCF file.
Variants are shown according to their heteroplasmic fraction (HF), plotting variants with HF = 1.0 on the outer border of the mitochondrial circle, those with HF = 0.0 on the inner border and all the others according to their actual HF value.
If the HF information is not available, variants will all be shown in the middle of the mitochondrial circle.
Usage
mitoviz can be used both from the command line and as a python module.
Command Line
Given a VCF file with human mitochondrial variants (sample.vcf), plotting them is fairly simple:
$ mitoviz sample.vcf
An image named mitoviz.png will be created in the current directory.
If you want to provide a specific filename where the plot will be saved, just add the --output option with the desired path:
$ mitoviz sample.vcf --output my_mt_plot.png
Python Module
Import mitoviz and use its plot_vcf function to use it in your own script:
from mitoviz import plot_vcf my_plot = plot_vcf("sample.vcf")
In this case, no plot will be shown until a call to plt.show() is made. It is possible to save the resulting plot using the save option and to provide a specific file where the plot will be saved using the output option:
from mitoviz import plot_vcf plot_vcf("sample.vcf", save=True, output="my_mt_plot.png")
Please refer to the Usage section of the documentation for further information.
Installation
PLEASE NOTE: HmtNote only supports Python >= 3.6!
The preferred installation method for mitoviz is using pip:
$ pip install mitoviz
Please refer to the Installation section of the documentation for further information.
Credits
This package was created with Cookiecutter and the cc-pypackage project template.
History
0.1.0 (2019-12-27)
First release.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for mitoviz-0.1.0-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 748b5af2e34efcf0ab109bb708123608a169b917119ae04cf56950e6019ffa76 |
|
MD5 | be040289ffd02bc135dea2969dd5f420 |
|
BLAKE2b-256 | 7c7b3616397f8fc78c330391fa621db874f441b03faa88aa3f285ee0e1a6cd1f |