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

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

.. _sphx_glr_auto_examples_plot_paired_strand_specific_bigwigs.py:


===================================
Paired Strand-Specific BigWig Track
===================================

Create a :class:`~pygv.tracks.bigwig_track.PairedStrandSpecificTrack` to show signals
on the forward strand (``pl_track``) and the reverse strand (``mn_track``).
This can be useful for presenting data from TSS-assays like GRO-cap/PRO-cap, NETCAGE, etc
and NascentTranscript-assays like PRO-seq, TT-seq, etc.

.. GENERATED FROM PYTHON SOURCE LINES 11-48



.. image-sg:: /auto_examples/images/sphx_glr_plot_paired_strand_specific_bigwigs_001.png
   :alt: chr1
   :srcset: /auto_examples/images/sphx_glr_plot_paired_strand_specific_bigwigs_001.png, /auto_examples/images/sphx_glr_plot_paired_strand_specific_bigwigs_001_2_00x.png 2.00x
   :class: sphx-glr-single-img


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

 .. code-block:: none


    array([<Axes: title={'center': 'chr1'}, ylabel='GRO-cap'>,
           <Axes: ylabel='GRO-cap'>, <Axes: ylabel='Color change'>,
           <Axes: ylabel='Bar'>], dtype=object)





|

.. code-block:: Python

    from pygv.viewer import GenomeViewer
    from pygv.tracks.bigwig_track import PairedStrandSpecificTrack
    gv = GenomeViewer()

    # draw positive and negative values independently
    independent_track = PairedStrandSpecificTrack(
        "../examples/data/K562_GROcap_hg38_pl.chr1.bw",
        "../examples/data/K562_GROcap_hg38_mn.chr1.bw",
        draw_y_independently=True,
        name="GRO-cap", y_label_rotation="vertical", y_label_ha="center")
    gv.add_track(independent_track)

    # draw positive and negative values like usual
    dependent_track = PairedStrandSpecificTrack(
        "../examples/data/K562_GROcap_hg38_pl.chr1.bw",
        "../examples/data/K562_GROcap_hg38_mn.chr1.bw",
        draw_y_independently=False,
        name="GRO-cap", y_label_rotation="vertical", y_label_ha="center")
    gv.add_track(dependent_track)

    # change the colors for signals on the two strands:
    diff_color_track = PairedStrandSpecificTrack(
        "../examples/data/K562_GROcap_hg38_pl.chr1.bw",
        "../examples/data/K562_GROcap_hg38_mn.chr1.bw",
        draw_y_independently=True, pos_color="#118ab2", neg_color="#ef476f",
        name="Color change", y_label_rotation="vertical", y_label_ha="center")
    gv.add_track(diff_color_track)

    # Bar plot
    bar_track = PairedStrandSpecificTrack(
        "../examples/data/K562_GROcap_hg38_pl.chr1.bw",
        "../examples/data/K562_GROcap_hg38_mn.chr1.bw",
        plot_type="bar", draw_y_independently=True, pos_color="#118ab2", neg_color="#ef476f",
        name="Bar", y_label_rotation="vertical", y_label_ha="center")
    gv.add_track(bar_track)

    gv.plot("chr1", 201954851, 201955948)


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

   **Total running time of the script:** (0 minutes 0.235 seconds)


.. _sphx_glr_download_auto_examples_plot_paired_strand_specific_bigwigs.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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