:orphan:

PyGV Track Gallery
==================


.. raw:: html

  <div id='sg-tag-list' class='sphx-glr-tag-list'></div>


.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a ReadArcTrack to show spliced reads from a BAM file. In contrast to SplicedReadTrack, this track shows the spliced parts as arcs.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_bam_arc_reads_thumb.png
    :alt:

  :doc:`/auto_examples/plot_bam_arc_reads`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Read alignment track with split parts joined by arcs</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a CollapsedReadTrack to show aligned reads in a BAM file.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_bam_collapsed_reads_thumb.png
    :alt:

  :doc:`/auto_examples/plot_bam_collapsed_reads`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Collapsed reads track</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a CoverageTrack.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_bam_coverage_thumb.png
    :alt:

  :doc:`/auto_examples/plot_bam_coverage`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Coverage track for a BAM file</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a StrandSpecificCoverageTrack to show the strand-specific coverage information in a BAM file.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_bam_stranded_coverage_thumb.png
    :alt:

  :doc:`/auto_examples/plot_bam_stranded_coverage`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Strand-specific coverage track for a BAM file</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a SplicedReadTrack to show the alignment in a BAM file, the spliced parts will be rendered as thinner lines.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_bam_spliced_reads_thumb.png
    :alt:

  :doc:`/auto_examples/plot_bam_spliced_reads`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Read alignment track with split parts joined by thinner lines</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a OverlayingTrack to show signals from multiple BigWig files within a single track.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_overlaying_bigwigs_thumb.png
    :alt:

  :doc:`/auto_examples/plot_overlaying_bigwigs`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Overlaying BigWig Tracks</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we will use PyGV to plot the sine function in a certain range.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_dyn_track_thumb.png
    :alt:

  :doc:`/auto_examples/plot_dyn_track`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Dynamic value track</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a simple BigWigTrack Track.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_bigwig_thumb.png
    :alt:

  :doc:`/auto_examples/plot_bigwig`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">BigWig Track</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a BigBed6Track.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_bigbed_thumb.png
    :alt:

  :doc:`/auto_examples/plot_bigbed`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">BigBed Track</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Directed BEDPE Track">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_bedpe_direction_thumb.png
    :alt:

  :doc:`/auto_examples/plot_bedpe_direction`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Directed BEDPE Track</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="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.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_logo_thumb.png
    :alt:

  :doc:`/auto_examples/plot_logo`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Sequence Logo Track</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="By default, the y-ticks are aligned to the center of the tick lines. If you want to plot the tick labels strictly inside the track, you can use the pygv.tracks.track.Track.inward_yticks property.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_inward_yticks_thumb.png
    :alt:

  :doc:`/auto_examples/plot_inward_yticks`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Inward y-ticks</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="By calling set_highlight_regions method, you can highlight multiple regions on each track.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_highlight_regions_thumb.png
    :alt:

  :doc:`/auto_examples/plot_highlight_regions`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Highlight regions on all tracks</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a PairedStrandlessTracks to show signals on the forward strand (``pl_track``) and the reverse strand (``mn_track``) in a strandless-manner. 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.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_paired_strandless_bigwigs_thumb.png
    :alt:

  :doc:`/auto_examples/plot_paired_strandless_bigwigs`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Paired Strandless BigWig Track</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="BEDPE Track">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_bedpe_thumb.png
    :alt:

  :doc:`/auto_examples/plot_bedpe`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">BEDPE Track</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="A shared scale can be applied to multiple numerical tracks via GenomeViewer&#x27;s add_group_autoscale method.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_group_autoscale_thumb.png
    :alt:

  :doc:`/auto_examples/plot_group_autoscale`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Apply the same scale to multiple tracks</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="A shared scale can be applied to multiple numerical tracks via GenomeViewer&#x27;s add_group_autoscale method.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_group_label_thumb.png
    :alt:

  :doc:`/auto_examples/plot_group_label`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Apply the same scale to multiple tracks</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a BedTrack.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_bed_thumb.png
    :alt:

  :doc:`/auto_examples/plot_bed`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Bed Track</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Adjust the number of feature lanes allowed">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_allowed_feature_lanes_thumb.png
    :alt:

  :doc:`/auto_examples/plot_allowed_feature_lanes`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Adjust the number of feature lanes allowed</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Create a 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.">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_paired_strand_specific_bigwigs_thumb.png
    :alt:

  :doc:`/auto_examples/plot_paired_strand_specific_bigwigs`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Paired Strand-Specific BigWig Track</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Apply data transformation to the original signal">

.. only:: html

  .. image:: /auto_examples/images/thumb/sphx_glr_plot_data_transform_thumb.png
    :alt:

  :doc:`/auto_examples/plot_data_transform`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Apply data transformation to the original signal</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /auto_examples/plot_bam_arc_reads
   /auto_examples/plot_bam_collapsed_reads
   /auto_examples/plot_bam_coverage
   /auto_examples/plot_bam_stranded_coverage
   /auto_examples/plot_bam_spliced_reads
   /auto_examples/plot_overlaying_bigwigs
   /auto_examples/plot_dyn_track
   /auto_examples/plot_bigwig
   /auto_examples/plot_bigbed
   /auto_examples/plot_bedpe_direction
   /auto_examples/plot_logo
   /auto_examples/plot_inward_yticks
   /auto_examples/plot_highlight_regions
   /auto_examples/plot_paired_strandless_bigwigs
   /auto_examples/plot_bedpe
   /auto_examples/plot_group_autoscale
   /auto_examples/plot_group_label
   /auto_examples/plot_bed
   /auto_examples/plot_allowed_feature_lanes
   /auto_examples/plot_paired_strand_specific_bigwigs
   /auto_examples/plot_data_transform


.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-gallery

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

      :download:`Download all examples in Python source code: auto_examples_python.zip </auto_examples/auto_examples_python.zip>`

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

      :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip </auto_examples/auto_examples_jupyter.zip>`


.. only:: html

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

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