.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "gallery/biology/plot_tca_cycle.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_tca_cycle.py>`
        to download the full example code.

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

.. _sphx_glr_gallery_biology_plot_tca_cycle.py:


TCA cycle
=========

This example visualises a subset of the tricarboxylic acid (TCA) cycle, also known as the Krebs cycle or citric acid cycle.

.. GENERATED FROM PYTHON SOURCE LINES 8-119



.. image-sg:: /gallery/biology/images/sphx_glr_plot_tca_cycle_001.png
   :alt: plot tca cycle
   :srcset: /gallery/biology/images/sphx_glr_plot_tca_cycle_001.png
   :class: sphx-glr-single-img





.. code-block:: Python


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



    g = nx.DiGraph()
    g.add_edges_from([
        ("oxaloacetate", "citrate"),
        ("citrate", "isocitrate"),
        ("isocitrate", "alpha-ketoglutarate"),
        ("alpha-ketoglutarate", "succinyl-CoA"),
        ("succinyl-CoA", "succinate"),
        ("succinate", "fumarate"),
        ("fumarate", "malate"),
        ("malate", "oxaloacetate"),
    ])
    edge_labels = {
        (u, v): str(i+1) for i, (u, v) in enumerate(g.edges)
    }


    layout = pd.DataFrame(nx.circular_layout(g)).T
    layout.iloc[:] = layout.values @ np.array([[0, -1], [1, 0]])
    layout[1] *= -1

    g.add_edges_from([
        ("acetyl CoA", "CoA-SH"),
        ("NAD+", "NADH"),
        ("NAD+ ", "NADH "),
        ("NAD+  ", "NADH  "),
        ("GDP", "GTP"),
        ("GTP", "GDP"),
        ("ADP", "ATP"),
    ])

    layout.loc["acetyl CoA"] = [0.27, 1.18]
    layout.loc["CoA-SH"] = [0.75, 1.05]
    layout.loc["NAD+"] = [0.68, -0.15]
    layout.loc["NADH"] = [0.61, -0.45]
    layout.loc["NAD+ "] = [0.65, -1.03]
    layout.loc["NADH "] = [0.35, -1.2]
    layout.loc["NAD+  "] = [-0.65, 1.03]
    layout.loc["NADH  "] = [-0.35, 1.2]
    layout.loc["GDP"] = [-0.25, -1.18]
    layout.loc["GTP"] = [-0.7, -0.98]
    layout.loc["ATP"] = [-0.35, -1.45]
    layout.loc["ADP"] = [-0.8, -1.25]

    edge_tension = {
        ("oxaloacetate", "citrate"): -0.8,
        ("citrate", "isocitrate"): -0.8,
        ("isocitrate", "alpha-ketoglutarate"): -0.8,
        ("alpha-ketoglutarate", "succinyl-CoA"): -0.8,
        ("succinyl-CoA", "succinate"): -0.8,
        ("succinate", "fumarate"): -0.8,
        ("fumarate", "malate"): -0.8,
        ("malate", "oxaloacetate"): -0.8,
        ("acetyl CoA", "CoA-SH"): 5.7,
        ("NAD+", "NADH"): -10.0,
        ("NAD+ ", "NADH "): 8.0,
        ("NAD+  ", "NADH  "): 8.0,
        ("GDP", "GTP"): 4.0,
        ("GTP", "GDP"): 3.2,
        ("ADP", "ATP"): -3.2,
    }

    edge_color = defaultdict(
        lambda: "black",
        {
            ("acetyl CoA", "CoA-SH"): "tomato",
            ("ADP", "ATP"): "gold",
        },
    )

    vertex_facecolor = defaultdict(
        lambda: "white",
        {
            "acetyl CoA": "tomato",
            "CoA-SH": "tomato",
            "ADP": "gold",
            "ATP": "gold",
        },
    )

    for (u, v) in g.edges:
        if (u, v) not in edge_labels:
            edge_labels[(u, v)] = ""


    # Visualise
    fig, ax = plt.subplots(figsize=(7, 8.5))
    ipx.network(
        g,
        layout=layout,
        ax=ax,
        style="hollow",
        vertex_labels=True,
        edge_curved=True,
        edge_tension=edge_tension,
        edge_labels=edge_labels,
        edge_label_rotate=True,
        edge_color=edge_color,
        vertex_facecolor=vertex_facecolor,
        vertex_alpha=0.7,
    )
    fig.tight_layout()


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

   **Total running time of the script:** (0 minutes 0.183 seconds)


.. _sphx_glr_download_gallery_biology_plot_tca_cycle.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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