https://github.com/aanastasiou/pymotifcounter

Python interface to the motif counting algorithms mfinder, fanmod, pgd, NetMODE
https://github.com/aanastasiou/pymotifcounter

bioinformatics graph-algorithms graph-theory networks python3 scientific-computing

Last synced: 2 months ago
JSON representation

Python interface to the motif counting algorithms mfinder, fanmod, pgd, NetMODE

• Host: GitHub
• URL: https://github.com/aanastasiou/pymotifcounter
• Owner: aanastasiou
• License: apache-2.0
• Created: 2021-10-22T09:11:19.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2023-07-17T14:17:05.000Z (over 1 year ago)
• Last Synced: 2024-04-28T00:23:08.826Z (8 months ago)
• Topics: bioinformatics, graph-algorithms, graph-theory, networks, python3, scientific-computing
• Language: C
• Homepage:
• Size: 1010 KB
• Stars: 4
• Watchers: 2
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
==============

PyMotifCounter

==============

A unified Python interface to fast motif enumeration algorithms such as:

* ``mfinder``

* ``fanmod``

* ``NetMODE``

* ``PGD``

A typical usage example is as follows:

.. code-block:: Python

    """

    Visualise the distribution of size-3 motifs.

    """

    from pymotifcounter.concretecounters import PyMotifCounterMfinder

    from matplotlib import pyplot as plt

    from networkx import watts_strogatz_graph

    if __name__ == "__main__":

        # Create an example network

        g = watts_strogatz_graph(100, 8, 0.2)

        # Create a motif counter based on mfinder

        motif_counter = PyMotifCounterMfinder()

        # Enumerate motifs using the selected counter

        g_mtf_count = motif_counter(g)

        # Visualise the distribution

        g_mtf_count.plot.bar("motif_id", "nreal")

        plt.tight_layout()

        plt.show()

Which would produce the following distribution:

.. image:: https://github.com/aanastasiou/pymotifcounter/blob/main/doc/source/resources/figures/fig_dist_motif_3.png?raw=true

Installation

------------

* Latest release can be installed from pypi by ``> pip install pymotifcounter``.

* Latest development version can be obtained by `cloning this repository `_

* For more details please see `the project's documentation on readthedocs `_