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

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

.. _sphx_glr_auto_examples_visualization_plot_clonal.py:


Visualizing a tree in clonal format
-----------------------------------

This example shows how to visualize an inferred tree.

.. GENERATED FROM PYTHON SOURCE LINES 7-12

.. code-block:: Python


    import scphylo as scp

    # sphinx_gallery_thumbnail_path = "_static/thumbnails/clonal.png"








.. GENERATED FROM PYTHON SOURCE LINES 13-14

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

.. GENERATED FROM PYTHON SOURCE LINES 14-18

.. code-block:: Python

    inferred = scp.io.read(
        scp.ul.get_file("scphylo.datasets/test/fp_0-fn_0-na_0.ground.CFMatrix")
    )








.. GENERATED FROM PYTHON SOURCE LINES 19-20

Next we convert the inferred genotype matrix to a tree object.

.. GENERATED FROM PYTHON SOURCE LINES 20-22

.. code-block:: Python

    tree = scp.ul.to_tree(inferred)








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Then we can draw the tree in `clonal` format i.e. mutations at the edges and cells at
at the nodes of the tree.

.. GENERATED FROM PYTHON SOURCE LINES 25-28

.. code-block:: Python


    # scp.pl.clonal_tree(tree)
    # TODO: fix








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

   **Total running time of the script:** (0 minutes 0.467 seconds)

**Estimated memory usage:**  9 MB


.. _sphx_glr_download_auto_examples_visualization_plot_clonal.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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