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

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

.. _sphx_glr_auto_examples_plot_logo.py:


===================
Sequence Logo Track
===================

A sequence logo is a graphical representation of the
sequence conservation and variation in a set of aligned sequences,
typically representing a group of related DNA, RNA, or protein sequences.
The primary purpose of a sequence logo is to visualize the sequence motifs
or patterns that are conserved across the aligned sequences.

In PyGV, you can create a :class:`~pygv.tracks.logo_track.LogoTrack` to show Sequence Logos.

.. GENERATED FROM PYTHON SOURCE LINES 14-37



.. image-sg:: /auto_examples/images/sphx_glr_plot_logo_001.png
   :alt: chr19
   :srcset: /auto_examples/images/sphx_glr_plot_logo_001.png, /auto_examples/images/sphx_glr_plot_logo_001_2_00x.png 2.00x
   :class: sphx-glr-single-img





.. code-block:: Python

    import pandas as pd
    import matplotlib.pyplot as plt
    import numpy as np
    from pygv.viewer import GenomeViewer
    from pygv.tracks.track import DynamicValueTrack
    from pygv.tracks.logo_track import LogoTrack


    gv = GenomeViewer()

    track = LogoTrack("", name="logo")
    gv.add_track(track)

    dyn_track = DynamicValueTrack("", name="data")
    gv.add_track(dyn_track)

    demo_start = 10000
    demo_end = 10129
    track.values = pd.read_csv("../examples/data/saliency.csv", index_col=0)
    dyn_track.values = np.sin(np.arange(demo_end-demo_start))
    gv.plot("chr19", demo_start, demo_end)
    plt.tight_layout()
    plt.show()


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

   **Total running time of the script:** (0 minutes 0.832 seconds)


.. _sphx_glr_download_auto_examples_plot_logo.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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