pyranges-plot 0.0.25

'Genomic intervals data visualization package for dataframe objects generated with PyRanges.'

pyranges_plot

Gene visualization package for dataframe objects generated with PyRanges.

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 Pyranges Plot is >= 1.0.0 (find it at https://github.com/pyranges/pyranges_1.x.git).

To obtain the plot there are some features to be defined by the user, one is the engine since it can be based on Matplotlib or Plotly, the other is optional and refers to the name of the gene ID column in your data. The rest of features can either be left as default or be customized. In example, the plot shows the first 25 genes of the dataframe by default, but this can be modified.

In the case of coloring, Pyranges Plot offers a wide versatility. The data feature (column) according to which the genes will be colored is by default the gene ID, but this "color column" can be selected manually. Color specifications can be left as the default colormap or be provided as dictionaries, lists or color objects from either Matplotlib or Plotly regardless of the chosen engine. When a colormap or list of colors is specified, the colors assigned to the genes will iterate over the provided ones following the color column pattern. In the case of concrete color instructions such as dictionary, the genes will be colored according to it while the non-specified ones will be colored in black.

Installation

PyRanges-Plot 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 pyranges-plot[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 pyranges-plot[plt]

# For plotly
pip install pyranges-plot[plotly]

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

Documentation

Pyranges Plot documentation and tutorial can be found at readthedocs.

Coming soon

• Bases will be displayed along coordinates.