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

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

.. _sphx_glr_auto_examples_plot_bam_coverage.py:


=============================
Coverage track for a BAM file
=============================

Create a :class:`~pygv.tracks.bam_track.CoverageTrack`.

.. GENERATED FROM PYTHON SOURCE LINES 8-16



.. image-sg:: /auto_examples/images/sphx_glr_plot_bam_coverage_001.png
   :alt: chr22
   :srcset: /auto_examples/images/sphx_glr_plot_bam_coverage_001.png, /auto_examples/images/sphx_glr_plot_bam_coverage_001_2_00x.png 2.00x
   :class: sphx-glr-single-img


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

 .. code-block:: none


    [<Axes: title={'center': 'chr22'}, ylabel='RNA-seq'>]





|

.. code-block:: Python

    from pygv.viewer import GenomeViewer
    from pygv.tracks.bam_track import CoverageTrack
    gv = GenomeViewer()
    track = CoverageTrack(
        "../examples/data/s03.chr22.bam",
        name="RNA-seq", y_label_rotation="vertical", y_label_ha="center")
    gv.add_track(track)
    gv.plot("chr22", 40345142, 40367239)


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

   **Total running time of the script:** (0 minutes 0.101 seconds)


.. _sphx_glr_download_auto_examples_plot_bam_coverage.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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