.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/enrichment_profile_overlay_example.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        Click :ref:`here <sphx_glr_download_auto_examples_enrichment_profile_overlay_example.py>`
        to download the full example code

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

.. _sphx_glr_auto_examples_enrichment_profile_overlay_example.py:


Enrichment Profile Overlay
=================================

Aggregate fraction of methylated bases centered at regions of interest defined in bed files.

.. GENERATED FROM PYTHON SOURCE LINES 9-10

Create (1) aggregate profile plots for mA/A and mCG/CG, (2) single-molecule plots for mA + mCG, and (3) base abundance plots for A and CG.

.. GENERATED FROM PYTHON SOURCE LINES 12-14

1. Python option
----------------

.. GENERATED FROM PYTHON SOURCE LINES 14-24

.. code-block:: default

    import dimelo as dm

    bam = "deep_ctcf_mod_mappings_merge.sorted.bam"
    sampleNames = ["q4", "q3", "q2", "q1"]
    beds = ["quart4.bed", "quart3.bed", "quart2.bed", "quart1.bed"]
    outDir = "./out"
    dm.plot_enrichment_profile(
        bam, sampleNames, beds, "A", outDir, threshA=190, dotsize=0.05
    )


.. GENERATED FROM PYTHON SOURCE LINES 25-28

2. Command line option
----------------------
``dimelo-plot-enrichment-profile -f deep_ctcf_mod_mappings_merge.sorted.bam -s q4 q3 q2 q1 -b quart4.bed quart3.bed quart2.bed quart1.bed -m A -o ./out -A 190 -d 0.05``

.. GENERATED FROM PYTHON SOURCE LINES 30-34

Output
----------------------
.. figure:: ../auto_examples/images/sample_deep_ctcf_mod_mappings_merge.sorted_A_sm_rolling_avg_overlay.png
    :align: center


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

   **Total running time of the script:** ( 0 minutes  0.000 seconds)


.. _sphx_glr_download_auto_examples_enrichment_profile_overlay_example.py:


.. only :: html

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



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

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



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

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


.. only:: html

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

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