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

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

.. _sphx_glr_auto_examples_plot_data_transform.py:


================================================
Apply data transformation to the original signal
================================================

.. GENERATED FROM PYTHON SOURCE LINES 8-43



.. image-sg:: /auto_examples/images/sphx_glr_plot_data_transform_001.png
   :alt: chr1
   :srcset: /auto_examples/images/sphx_glr_plot_data_transform_001.png, /auto_examples/images/sphx_glr_plot_data_transform_001_2_00x.png 2.00x
   :class: sphx-glr-single-img


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

 .. code-block:: none

    /home/docs/checkouts/readthedocs.org/user_builds/pygv/checkouts/latest/pygv/tracks/track.py:840: RuntimeWarning: invalid value encountered in multiply
      x = (x >= 0) * x + (x < 0) * x * a






|

.. code-block:: Python

    import matplotlib.pyplot as plt
    import numpy as np
    from pygv.viewer import GenomeViewer
    from pygv.tracks.bigwig_track import PairedStrandSpecificTracks
    gv = GenomeViewer()

    # For this track, we don't apply any transformation
    notrans_track = PairedStrandSpecificTracks(
        "../examples/data/K562_GROcap_hg38_pl.chr1.bw",
        "../examples/data/K562_GROcap_hg38_mn.chr1.bw",
        draw_y_independently=True,
        name="Original", y_label_rotation="vertical", y_label_ha="center")
    gv.add_track(notrans_track)
    # For this track, we apply inverse hyperbolic sine transformation
    # this transformation is similar to log, but it allows for negative values
    asinh_track = PairedStrandSpecificTracks(
        "../examples/data/K562_GROcap_hg38_pl.chr1.bw",
        "../examples/data/K562_GROcap_hg38_mn.chr1.bw",
        draw_y_independently=True,
        name="Asinh", y_label_rotation="vertical", y_label_ha="center")
    asinh_track.data_transform = "asinh"
    gv.add_track(asinh_track)
    # Finally, we apply a customized function (sliding sum)
    sliding_sum_track = PairedStrandSpecificTracks(
        "../examples/data/K562_GROcap_hg38_pl.chr1.bw",
        "../examples/data/K562_GROcap_hg38_mn.chr1.bw",
        draw_y_independently=True,
        name="Customized\nfunc", y_label_rotation="vertical", y_label_ha="center")
    # Define a function to calculate the sliding sum (window size: 49)
    # the following function requires numpy version >= 1.20.0
    sliding_sum_track.data_transform = lambda x: np.pad(
        np.lib.stride_tricks.sliding_window_view(x, 49).sum(axis=-1), (24, 24))
    gv.add_track(sliding_sum_track)
    gv.plot("chr1", 201954851, 201955948)
    plt.tight_layout()


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

   **Total running time of the script:** (0 minutes 0.247 seconds)


.. _sphx_glr_download_auto_examples_plot_data_transform.py:

.. only:: html

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

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

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

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

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

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

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


.. only:: html

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

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