Pyrangeyes

Gene visualization package for dataframe objects generated with PyRanges.

Pyrangeyes significantly facilitates genomic data interpretation by providing powerful, customizable, and user-friendly visualizations. It effectively covers the gap between data manipulation and visualization, thereby accelerating the analysis workflow in genomic research.

Overview

The goal is getting a plot displaying a series of genes, transcripts, or any kind of ranges contained in a PyRanges object. It displays the genes' intron-exon structure in its corresponding chromosome, enabling easy visualization of your PyRanges data. The Pyranges version compatible with Pyrangeyes is >= 1.0.0 (find it at https://github.com/pyranges/pyranges_1.x.git).

To obtain a plot, the variable engine must be specified by the user first. This variable defines the graphic library on which the plots will be based: the valid engine options are "matplotlib" or "plt" for Matplotlib and "plotly" or "ply" for Plotly.

Every other functionality can be defined during the plot function call. These functionalities include the ID column to group the intervals belonging to the same item (transcript, gene, protein...), items disposition, coloring criteria and palette, labels, row ordering (sort_ranges=True for genomic sorting), and output form among others. The input for the plot function is 1 or more PyRanges objects, and the output is by default an interactive plot with zooming options and tooltip information, but if desired the plot can be directly exported to a png or pdf file.

Installation

Pyrangeyes can be installed using pip. To install all dependencies in order to be able to use all the functionalities of the package and both engines, the [all] option must be specified:

pip install pyrangeyes[all]

If the user wishes to use only one of the engines, the installation of all dependencies can be avoided by using the engine-specific installation options:

# For matplotlib
pip install pyrangeyes[matplotlib]

# For plotly
pip install pyrangeyes[plotly]

Note that the minimal installation by pip install pyrangeyes is not able to produce plots since the graphical dependencies are not installed.

Documentation

Pyrangeyes documentation and tutorial can be found at https://pyrangeyes.readthedocs.io/.