============
Bed Analysis
============

Analyses related to bed-files, where the peaks are located with respect to genes, how multiple bed-files overlap, or to
get a mapping of overlapping peaks between files and genes and more.
Centred on the usage of `pybedtools <https://daler.github.io/pybedtools/>`_, but also works with stored bed-files.
To run the example code for this module, we will always start with this block of code:

.. code-block:: python

    *Bed_Analysis.base_code*

.. .--------------------------------------------------------------------------------------------------------------------
.. gene_location_bpwise
.. .--------------------------------------------------------------------------------------------------------------------
.. autofunction:: Bed_Analysis.gene_location_bpwise

.. code-block:: python

    *Bed_Analysis.gene_location_bpwise*

|pic1| |pic2|

.. |pic1| image:: gallery/Example_peaks_GeneFeatureLocation_bpwiseOverlap_PieChart.png
   :width: 45%

.. |pic2| image:: gallery/InclExternalExample_peaks_GeneFeatureLocation_bpwiseOverlap_PieChart.png
   :width: 45%

.. .--------------------------------------------------------------------------------------------------------------------
.. intersection_heatmap
.. .--------------------------------------------------------------------------------------------------------------------
.. autofunction:: Bed_Analysis.intersection_heatmap

.. image:: gallery/IGV_MultiBed.png
   :width: 90%

.. code-block:: python

    *Bed_Analysis.intersection_heatmap*

.. image:: gallery/_MultiIntersectHeat.png
   :width: 90%

.. code-block:: python

    *Bed_Analysis.intersection_heatmap_fisher*

Don't expect a very meaningful result here. The data is limited to chr1 and the activity filter of the peaks per cell type rather crude. Also,
please note that if you do overlap with SNVs, you should consider their linkage disequilibrium structure.

|pic3| |pic4|

.. |pic3| image:: gallery/HockerATAC_MultiIntersectHeat.png
   :width: 45%

.. |pic4| image:: gallery/HockerATAC_MultiIntersectHeat_Fisher.png
   :width: 45%

.. .--------------------------------------------------------------------------------------------------------------------
.. upset_to_reference
.. .--------------------------------------------------------------------------------------------------------------------
.. autofunction:: Bed_Analysis.upset_to_reference

.. code-block:: python

    *Bed_Analysis.upset_to_reference*

.. image:: gallery/_UpSet_Subset_peaks.png
   :width: 80%

.. .--------------------------------------------------------------------------------------------------------------------
.. peaks_peaks_overlap
.. .--------------------------------------------------------------------------------------------------------------------
.. autofunction:: Bed_Analysis.peaks_peaks_overlap

.. code-block:: python

    *Bed_Analysis.peaks_peaks_overlap*

.. include:: gallery/src.Bed_Analysis.peaks_peaks_overlap.txt
    :literal:

.. .--------------------------------------------------------------------------------------------------------------------
.. peaks_promoter_overlap
.. .--------------------------------------------------------------------------------------------------------------------
.. autofunction:: Bed_Analysis.peaks_promoter_overlap

.. code-block:: python

    *Bed_Analysis.peaks_promoter_overlap*

.. include:: gallery/src.Bed_Analysis.peaks_promoter_overlap.txt
    :literal:

.. .--------------------------------------------------------------------------------------------------------------------
.. peaks_fetch_col
.. .--------------------------------------------------------------------------------------------------------------------
.. autofunction:: Bed_Analysis.peaks_fetch_col

.. code-block:: python

    *Bed_Analysis.peaks_fetch_col1*

Take a look at the example ATAC peaks and the files defined by the file system pattern.
BaseATAC_peaks.txt

.. include:: ../ExampleData/BaseATAC_peaks.txt
    :literal:

DiffATAC/DiffATAC_Macs.txt

.. include:: ../ExampleData/DiffATAC/DiffATAC_Macs.txt
    :literal:

DiffATAC/DiffATAC_TCells.txt

.. include:: ../ExampleData/DiffATAC/DiffATAC_TCells.txt
    :literal:

.. code-block:: python

    *Bed_Analysis.peaks_fetch_col2*

.. include:: gallery/src.Bed_Analysis.peaks_fetch_col.txt
    :literal:

.. .--------------------------------------------------------------------------------------------------------------------
.. promoter_fetch_col
.. .--------------------------------------------------------------------------------------------------------------------
.. autofunction:: Bed_Analysis.promoter_fetch_col

.. code-block:: python

    *Bed_Analysis.promoter_fetch_col*

.. include:: gallery/src.Bed_Analysis.promoter_fetch_col.txt
    :literal:


.. .--------------------------------------------------------------------------------------------------------------------
.. peaks_genebody_overlap
.. .--------------------------------------------------------------------------------------------------------------------
.. autofunction:: Bed_Analysis.peaks_genebody_overlap

.. code-block:: python

    *Bed_Analysis.peaks_genebody_overlap*

.. include:: gallery/src.Bed_Analysis.peaks_genebody_overlap.txt
    :literal:


.. .--------------------------------------------------------------------------------------------------------------------
.. possible_interactions
.. .--------------------------------------------------------------------------------------------------------------------
.. autofunction:: Bed_Analysis.possible_interactions

.. code-block:: python

    *Bed_Analysis.possible_interactions*

.. include:: gallery/src.Bed_Analysis.possible_interactions.txt
    :literal: