.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "gallery/biology/plot_cell_cycle_arrest.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_gallery_biology_plot_cell_cycle_arrest.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_gallery_biology_plot_cell_cycle_arrest.py:


Cell cycle arrest
=================

This example visualises protein protein interactions involved in the "cell cycle arrest" pathway.

It also shows how to use ``iplotx`` to combine network plots with other matplotlib chart types.

.. GENERATED FROM PYTHON SOURCE LINES 9-61



.. image-sg:: /gallery/biology/images/sphx_glr_plot_cell_cycle_arrest_001.png
   :alt: plot cell cycle arrest
   :srcset: /gallery/biology/images/sphx_glr_plot_cell_cycle_arrest_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


    import numpy as np
    import pandas as pd
    import networkx as nx
    import matplotlib.pyplot as plt
    import iplotx as ipx


    node_data = pd.read_csv("data/cell_cycle_arrest_string_network_coordinates.tsv", sep="\t", index_col=0)
    edge_data = pd.read_csv("data/cell_cycle_arrest_string_interactions_short.tsv", sep="\t")

    g = nx.Graph()
    g.add_edges_from(edge_data.iloc[:, :2].values)

    layout = node_data[["x_position", "y_position"]]
    node_data["color_ipx"] = [list(map(lambda x: float(x) / 256.0, x[4:-1].split(","))) for x in node_data["color"]]
    node_data["label_color"] = ["white" if np.mean(x) < 0.4 else "black" for x in node_data["color_ipx"]]


    fig = plt.figure(figsize=(9, 6))
    ax = plt.subplot2grid((2, 3), (0, 0), colspan=2, rowspan=2)
    ax2 = plt.subplot2grid((2, 3), (0, 2))
    ax3 = plt.subplot2grid((2, 3), (1, 2))
    ipx.network(
        g,
        layout=layout,
        ax=ax,
        vertex_labels=True,
        vertex_marker="r",
        vertex_size="label",
        vertex_facecolor=node_data["color_ipx"].to_dict(),
        vertex_label_color=node_data["label_color"].to_dict(),
        vertex_edgecolor="k",
        vertex_linewidth=0.5,
        edge_alpha=0.2,
        vertex_zorder=3,

    )

    degrees = np.bincount(list(dict(g.degree()).values()))
    bindegs = np.arange(len(degrees))
    ax2.bar(bindegs, degrees, color="gray")
    ax2.set_xlabel("Node degree")
    ax2.set_ylabel("Number of\nproteins")

    pagerank = list(nx.pagerank(g).values())
    ax3.ecdf(pagerank, color="black", complementary=True)
    ax3.axvline(0.1, ls="--", lw=2, color="tomato")
    ax3.set_xlabel("Node PageRank")
    ax3.set_ylabel("Cumulative")

    fig.tight_layout()


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 0.238 seconds)


.. _sphx_glr_download_gallery_biology_plot_cell_cycle_arrest.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_cell_cycle_arrest.ipynb <plot_cell_cycle_arrest.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_cell_cycle_arrest.py <plot_cell_cycle_arrest.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_cell_cycle_arrest.zip <plot_cell_cycle_arrest.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_