:orphan:

General examples
================

.. contents::




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

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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows the full process to perform a complete SCA analysis and detect protein sectors from data importation, MSA filtering.">

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

  :ref:`sphx_glr_auto_examples_plot_simple_sca.py`

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      <div class="sphx-glr-thumbnail-title">The simplest SCA analysis ever</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we showcase how to create a pandas.DataFrame to map the original MSA&#x27;s positions with the PDB positions, PDB named position, the MSA filtered positions, and the sectors.">

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

  :ref:`sphx_glr_auto_examples_plot_map_alignments.py`

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      <div class="sphx-glr-thumbnail-title">Mapping original MSA, filtered MSA, PDB, and sectors</div>
    </div>


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    </div>


.. toctree::
   :hidden:

   /auto_examples/plot_simple_sca
   /auto_examples/plot_map_alignments

.. advanced_example:

Advanced usage of cocoatree
---------------------------



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    <div class="sphx-glr-thumbcontainer" tooltip="It is possible to perform Cocoatree&#x27;s SCA pipeline by defining it&#x27;s own metric. In this example, we show how to use a callable to compute the coevolution metric.">

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  .. image:: /auto_examples/advanced/images/thumb/sphx_glr_plot_sca_with_own_metric_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_advanced_plot_sca_with_own_metric.py`

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      <div class="sphx-glr-thumbnail-title">Running Cocoatree with your own metric</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In this example, we are comparing the results of the co-evolution analysis on serine proteases using SCA and the mutual information.">

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  .. image:: /auto_examples/advanced/images/thumb/sphx_glr_plot_sca_vs_mi_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_advanced_plot_sca_vs_mi.py`

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      <div class="sphx-glr-thumbnail-title">Mutual information versus SCA</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows the full process to perform a complete SCA analysis and detect protein sectors from data importation, MSA filtering.">

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  .. image:: /auto_examples/advanced/images/thumb/sphx_glr_plot_full_SCA_analysis_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_advanced_plot_full_SCA_analysis.py`

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      <div class="sphx-glr-thumbnail-title">Perform full SCA analysis on the S1A serine protease dataset</div>
    </div>


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    </div>

.. datasets_example:

Datasets
--------



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    <div class="sphx-glr-thumbcontainer" tooltip="Load the dataset">

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  .. image:: /auto_examples/datasets/images/thumb/sphx_glr_plot_rhomboid_proteases_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_datasets_plot_rhomboid_proteases.py`

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      <div class="sphx-glr-thumbnail-title">Rhomboid proteases</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Load the dataset">

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  .. image:: /auto_examples/datasets/images/thumb/sphx_glr_plot_DHFR_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_datasets_plot_DHFR.py`

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      <div class="sphx-glr-thumbnail-title">DHFR proteases</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Load the dataset">

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  .. image:: /auto_examples/datasets/images/thumb/sphx_glr_plot_s1A_serine_proteases_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_datasets_plot_s1A_serine_proteases.py`

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      <div class="sphx-glr-thumbnail-title">S1A serine proteases</div>
    </div>


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    </div>

.. visualization_example:

Visualization
-------------



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    <div class="sphx-glr-thumbcontainer" tooltip="A simple tree visualization with cocoatree.">

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  .. image:: /auto_examples/visualizations/images/thumb/sphx_glr_plot_simple_tree_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_visualizations_plot_simple_tree.py`

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      <div class="sphx-glr-thumbnail-title">Simple tree visualization with metadata</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="A small example that shows how to plot the sector composition within a tree and to add metadata">

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  .. image:: /auto_examples/visualizations/images/thumb/sphx_glr_plot_tree_metadata_sector_seq_and_coevol_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_visualizations_plot_tree_metadata_sector_seq_and_coevol.py`

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      <div class="sphx-glr-thumbnail-title">Plot sector together with (phylogenetic) tree and metadata</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="The user can provide a dictionnary of colors for metadata.">

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  .. image:: /auto_examples/visualizations/images/thumb/sphx_glr_plot_tree_metadata_colors_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_visualizations_plot_tree_metadata_colors.py`

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      <div class="sphx-glr-thumbnail-title">Specifying metadata's colors</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="A simple tree visualization with cocoatree.">

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  .. image:: /auto_examples/visualizations/images/thumb/sphx_glr_test_thumb.png
    :alt:

  :ref:`sphx_glr_auto_examples_visualizations_test.py`

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      <div class="sphx-glr-thumbnail-title">Simple tree visualization with metadata</div>
    </div>


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    </div>


.. toctree::
   :hidden:
   :includehidden:


   /auto_examples/advanced/index.rst
   /auto_examples/datasets/index.rst
   /auto_examples/visualizations/index.rst


.. 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>`_
