Plot variants on the human mitochondrial genome.
- Free software: MIT license
- Documentation: https://mitoviz.readthedocs.io
- GitHub repo: https://github.com/robertopreste/mitoviz
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 VCF and tabular files, as well as from general pandas
dataframes when importing
mitoviz in Python.
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 in between, 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.
A linear representation of the mitochondrial genome can also be plotted; in this case, variants are shown using a lollipop plot style, with the height of the marker reflecting their HF.
Variants with no HF information will be shown as if their HF was 0.5.
mitoviz can be used both from the command line and as a python module.
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
Linear plots can be created using the --linear
option:
$ mitoviz sample.vcf --linear
Polar and linear interactive plots can also be created by adding the --interactive
option, and
will be saved to an HTML file:
$ mitoviz sample.vcf --interactive
It is also possible to plot variants stored in a tabular file, such as CSV or TSV formats; mitoviz
will automatically recognise them, treating the file as comma-separated by default. If a different
separator is used (as in the case of TSV files), just specify it with the --sep
option:
$ mitoviz sample.tsv --sep "\t"
If you just need to create an empty mitochondrial plot, we've got you covered: use the
mitoviz-base
command and provide one or more options like --linear
, --interactive
,
--legend
, --split
, --output
, based on your needs.
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:
plot_vcf("sample.vcf", save=True, output="my_mt_plot.png")
By default, a polar plot is returned; linear plots are easily created using the linear
option:
plot_vcf("sample.vcf", save=True, linear=True)
Interactive plots can be created with the interactive
option, and can be either saved to an
HTML file or inspected in a Jupyter notebook:
# Show the interactive plot (works in a Jupyter notebook)
plot_vcf("sample.vcf", interactive=True)
# Save the interactive plot to an HTML file
plot_vcf("sample.vcf", interactive=True, save=True)
A similar function to plot variants contained in a pandas DataFrame is available as plot_df
.
Supposing you have a pandas DataFrame with human mitochondrial variants named variants_df
, it
is possible to plot them as follows:
from mitoviz import plot_df
plot_df(variants_df)
Variants stored in tabular files can be plotted using plot_table
, which accepts the same
options available for plot_vcf
and plot_df
, with the addition of sep
, which is used to
specify the column separator. By default, the comma is used as column delimiter:
from mitoviz import plot_table
# plotting a CSV file
plot_table("sample.csv")
# plotting a TSV (tab-separated) file
plot_table("sample.tsv", sep="\t")
plot_table
also accept additional keyword options, which will be passed to pandas.read_table
when processing the given input file:
plot_table("sample.tsv", sep="\t", comment="#", skiprows=0)
If you just need to create an empty mitochondrial plot, the plot_base
function allows to do so,
and accepts the linear
, interactive
, legend
, split
, output
and save
arguments to further tweak its behaviour.
Please refer to the Usage section of the documentation for further information.
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.
This package was created with Cookiecutter and the cc-pypackage project template.