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

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

.. _sphx_glr_auto_examples_assessment_compute_partf.py:


Reconstruct tree by Trisicell-PartF
-----------------------------------

This example shows how to assess a phylogenetic tree using Trisicell-PartF on a
binary single-cell genotype matrix.

.. GENERATED FROM PYTHON SOURCE LINES 8-13

.. code-block:: Python


    import scphylo as scp

    # sphinx_gallery_thumbnail_path = "_static/thumbnails/trisicell-partf.png"








.. GENERATED FROM PYTHON SOURCE LINES 14-15

First, we load a binary test single-cell genotype data.

.. GENERATED FROM PYTHON SOURCE LINES 15-18

.. code-block:: Python

    df_in = scp.datasets.test()
    df_in.head()






.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <div>
    <style scoped>
        .dataframe tbody tr th:only-of-type {
            vertical-align: middle;
        }

        .dataframe tbody tr th {
            vertical-align: top;
        }

        .dataframe thead th {
            text-align: right;
        }
    </style>
    <table border="1" class="dataframe">
      <thead>
        <tr style="text-align: right;">
          <th></th>
          <th>mut0</th>
          <th>mut1</th>
          <th>mut2</th>
          <th>mut3</th>
          <th>mut4</th>
          <th>mut5</th>
          <th>mut6</th>
          <th>mut7</th>
          <th>mut8</th>
          <th>mut9</th>
          <th>mut10</th>
          <th>mut11</th>
          <th>mut12</th>
          <th>mut13</th>
          <th>mut14</th>
          <th>mut15</th>
          <th>mut16</th>
          <th>mut17</th>
          <th>mut18</th>
          <th>mut19</th>
        </tr>
        <tr>
          <th>cellIDxmutID</th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
          <th></th>
        </tr>
      </thead>
      <tbody>
        <tr>
          <th>cell0</th>
          <td>1</td>
          <td>1</td>
          <td>1</td>
          <td>1</td>
          <td>1</td>
          <td>1</td>
          <td>1</td>
          <td>0</td>
          <td>3</td>
          <td>3</td>
          <td>0</td>
          <td>3</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>3</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
        </tr>
        <tr>
          <th>cell1</th>
          <td>3</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>3</td>
          <td>0</td>
          <td>1</td>
          <td>1</td>
          <td>3</td>
          <td>1</td>
          <td>0</td>
          <td>0</td>
          <td>3</td>
          <td>0</td>
          <td>0</td>
          <td>1</td>
          <td>1</td>
          <td>1</td>
        </tr>
        <tr>
          <th>cell2</th>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>1</td>
          <td>1</td>
          <td>3</td>
          <td>1</td>
          <td>1</td>
          <td>0</td>
          <td>0</td>
          <td>3</td>
          <td>1</td>
          <td>1</td>
          <td>1</td>
          <td>1</td>
          <td>0</td>
        </tr>
        <tr>
          <th>cell3</th>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>3</td>
          <td>1</td>
          <td>0</td>
          <td>0</td>
          <td>1</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>1</td>
          <td>1</td>
          <td>1</td>
          <td>0</td>
          <td>0</td>
        </tr>
        <tr>
          <th>cell4</th>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>1</td>
          <td>1</td>
          <td>1</td>
          <td>1</td>
          <td>1</td>
          <td>0</td>
          <td>0</td>
          <td>3</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
          <td>0</td>
        </tr>
      </tbody>
    </table>
    </div>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 19-21

Then, using :func:`scphylo.tl.partf` we calculate the probability of `cell6` and
`cell17` seeded by `mut12`

.. GENERATED FROM PYTHON SOURCE LINES 21-31

.. code-block:: Python

    probs = scp.tl.partition_function(
        df_in,
        alpha=0.000001,
        beta=0.1,
        n_samples=100,
        n_batches=10,
        muts=["mut12"],
        cells=["cell6", "cell17"],
    )
    probs.mean(axis=1).round(4).values[0]




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

 .. code-block:: none

    elapsed time: 0:00:04.770798

    0.8948




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

   **Total running time of the script:** (0 minutes 5.207 seconds)

**Estimated memory usage:**  10 MB


.. _sphx_glr_download_auto_examples_assessment_compute_partf.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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