CoMut

CoMut is a Python library for creating comutation plots to visualize genomic and phenotypic information.

Installation

The original version (v0.0.3) of comut is available on pypi here and can be installed via pip install comut.

This version is not yet available on pypi and may be installed via cloning of this repository on your session and then

pip install -e /path/to/this/repo

Colab Quickstart

For those who do not want to install Python or other packages, there is a Google Colab notebook where you can simply upload a MAF file and run the notebook to make a basic comutation plot. This file is also available as a jupyter notebook for local use.

Citation

CoMut is now published here. If you use CoMut in a paper, please cite:

Crowdis, J., He, M.X., Reardon, B. & Van Allen, E. M. CoMut: Visualizing integrated molecular information with comutation plots. Bioinformatics (2020). doi:10.1093/bioinformatics/btaa554

Documentation

There is also a Documentation notebook that provides documentation for CoMut. It describes the fundamentals of creating comutation plots and provides the code used to generate the comut above.

Development

If you would like to report a bug or request a feature, please do so using the issues page

Dependencies

CoMut runs on python 3.6 or later. CoMut requires the following packages as dependencies (they will be installed along with CoMut if using pip)

numpy>=1.18.1
pandas>=0.25.3
palettable>=3.3.0
matplotlib>=3.3.1

Versions

1.0.0 - Multiple changes

• Add arguments in the like of xtick_style, xtick_fontdict, xtick_show, xtick_rotation, xlabel, xlabel_fontsize, xlabel_fontweight to the functions add_categorical_data, add_continuous_data, add_bar_data.
• Add functions add_scatter_data, _plot_scatter_data for drawing symbols on selected tiles (see example 2 below).
• Add functions add_side_error_data, _plot_side_error_data for drawing an error bar plot (see example 4).
• Modify _plot_side_bar_data to allow for grouped bars in unstacked mode. Add arguments to the function add_side_bar_data to control for the heights and gaps between the bars.

0.0.3 - No code is changed, description updated for public release
0.0.2 - Introduce compatibility for Python 3.6
0.0.1 - Initial release

Examples

For the full code underlying these examples, see in tests/test_comut.

Example 1

Basic example.

Example 2

As compared to example 1, star symbols are added on certain cells and percentage labels were added on the left bar plot. Observe that the star sometimes are composed of 2 colors. Additionally, xtick labels of the central plot have been hidden.

Example 3

As compared to example 2, add a bar plot on the right.

Example 4

As compared to example 3, replace the right bar plot by a right error bar plot.

Example 5

As compared to example 4, add another bar plot right of the right bar plot.

Example 6

As compared to example 1, replace a simple bar plot by grouped bar plot.