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

.. only:: html

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

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

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

.. _sphx_glr_auto_examples_plot_seqalign.py:


Sequence Alignment Plot
=======================

.. GENERATED FROM PYTHON SOURCE LINES 5-18

.. code-block:: Python

    from collections import Counter
    import numpy as np
    import pandas as pd

    import marsilea as ma
    import marsilea.plotter as mp
    import matplotlib as mpl

    import mpl_fontkit as fk
    fk.install("Roboto Mono", verbose=False)

    mpl.rcParams["font.size"] = 30








.. GENERATED FROM PYTHON SOURCE LINES 19-21

Load data
---------

.. GENERATED FROM PYTHON SOURCE LINES 21-24

.. code-block:: Python

    seq = ma.load_data("seq_align")
    seq = seq.iloc[:, 130:175]








.. GENERATED FROM PYTHON SOURCE LINES 25-27

Calculate the height of each amino acid.
See https://en.wikipedia.org/wiki/Sequence_logo

.. GENERATED FROM PYTHON SOURCE LINES 27-50

.. code-block:: Python


    collect = []
    for _, col in seq.items():
        collect.append(Counter(col))

    hm = pd.DataFrame(collect)
    del hm["-"]
    hm = hm.T.fillna(0.0)
    hm.columns = seq.columns
    hm /= hm.sum(axis=0)

    n = hm.shape[1]
    s = 20
    En = (1 / np.log(2)) * ((s - 1) / (2 * n))

    heights = []
    for _, col in hm.items():
        H = -(np.log2(col) * col).sum()
        R = np.log2(20) - (H + En)
        heights.append(col * R)

    logo = pd.DataFrame(heights).T





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /home/docs/checkouts/readthedocs.org/user_builds/marsilea/envs/v0.3.2/lib/python3.10/site-packages/pandas/core/arraylike.py:399: RuntimeWarning: divide by zero encountered in log2
      result = getattr(ufunc, method)(*inputs, **kwargs)




.. GENERATED FROM PYTHON SOURCE LINES 51-53

Prepare color palette and data
------------------------------

.. GENERATED FROM PYTHON SOURCE LINES 53-96

.. code-block:: Python


    color_encode = {
        'A': '#f76ab4',
        'C': '#ff7f00',
        'D': '#e41a1c',
        'E': '#e41a1c',
        'F': '#84380b',
        'G': '#f76ab4',
        'H': '#3c58e5',
        'I': '#12ab0d',
        'K': '#3c58e5',
        'L': '#12ab0d',
        'M': '#12ab0d',
        'N': '#972aa8',
        'P': '#12ab0d',
        'Q': '#972aa8',
        'R': '#3c58e5',
        'S': '#ff7f00',
        'T': '#ff7f00',
        'V': '#12ab0d',
        'W': '#84380b',
        'Y': '#84380b',
        '-': 'white'
        }

    max_aa = []
    freq = []

    for _, col in hm.items():
        ix = np.argmax(col)
        max_aa.append(hm.index[ix])
        freq.append(col[ix])

    position = []
    mock_ticks = []
    for i in seq.columns:
        if int(i) % 10 == 0:
            position.append(i)
            mock_ticks.append("^")
        else:
            position.append("")
            mock_ticks.append("")





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /home/docs/checkouts/readthedocs.org/user_builds/marsilea/checkouts/v0.3.2/examples/plot_seqalign.py:84: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
      freq.append(col[ix])




.. GENERATED FROM PYTHON SOURCE LINES 97-99

Plot
----

.. GENERATED FROM PYTHON SOURCE LINES 99-115

.. code-block:: Python


    height = 5
    width = height * seq.shape[1] / seq.shape[0]

    ch = ma.CatHeatmap(seq.to_numpy(), palette=color_encode, height=height, width=width)
    ch.add_layer(ma.plotter.TextMesh(seq.to_numpy()))
    ch.add_top(ma.plotter.SeqLogo(logo, color_encode=color_encode), pad=.1, size=2)
    ch.add_left(ma.plotter.Labels(seq.index), pad=.1)
    ch.add_bottom(ma.plotter.Labels(mock_ticks, rotation=0), pad=.1)
    ch.add_bottom(ma.plotter.Labels(position, rotation=0))
    ch.add_bottom(ma.plotter.Numbers(freq, width=.9, color="#FFB11B", show_value=False),
                  name="freq_bar", size=2)
    ch.add_bottom(ma.plotter.Labels(max_aa, rotation=0), pad=.1)
    ch.render()

    ch.get_ax("freq_bar").set_axis_off()



.. image-sg:: /auto_examples/images/sphx_glr_plot_seqalign_001.png
   :alt: plot seqalign
   :srcset: /auto_examples/images/sphx_glr_plot_seqalign_001.png, /auto_examples/images/sphx_glr_plot_seqalign_001_2_00x.png 2.00x
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 11.654 seconds)


.. _sphx_glr_download_auto_examples_plot_seqalign.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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