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

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

.. _sphx_glr_auto_examples_visualization_plot_dendrogram.py:


Visualizing a tree in dendrogram 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/dendrogram.png"








.. GENERATED FROM PYTHON SOURCE LINES 13-14

First, we load a readcount single-cell genotype data and filter it.

.. GENERATED FROM PYTHON SOURCE LINES 14-24

.. code-block:: Python

    adata = scp.datasets.example()
    adata = adata[adata.obs.group.isin(["C16", "C11", "C22"]), :].copy()
    scp.pp.filter_mut_vaf_greater_than_coverage_mutant_greater_than(
        adata, min_vaf=0.4, min_coverage_mutant=20, min_cells=2
    )
    scp.pp.filter_mut_reference_must_present_in_at_least(adata, min_cells=1)
    scp.pp.filter_mut_mutant_must_present_in_at_least(adata, min_cells=2)
    scp.pp.build_scmatrix(adata)
    df_in = adata.to_df()





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

 .. code-block:: none

    /home/docs/checkouts/readthedocs.org/user_builds/scphylo-tools/envs/latest/lib/python3.9/site-packages/anndata/__init__.py:51: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.
      warnings.warn(
    Matrix with n_obs × n_vars = 21 × 123
    Matrix with n_obs × n_vars = 21 × 112
    Matrix with n_obs × n_vars = 21 × 112




.. GENERATED FROM PYTHON SOURCE LINES 25-26

Then we infer the tree using scistree algorithm.

.. GENERATED FROM PYTHON SOURCE LINES 26-28

.. code-block:: Python

    df_out = scp.tl.scistree(df_in, alpha=0.001, beta=0.2)





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

 .. code-block:: none

    running ScisTree with alpha=0.001, beta=0.2, n_threads=1
    input -- size: 21x112
    input -- 0: 817#, 34.7%
    input -- 1: 790#, 33.6%
    input -- NA: 745#, 31.7%
    input -- CF: False
    output -- size: 21x112
    output -- 0: 721#, 30.7%
    output -- 1: 1631#, 69.3%
    output -- NA: 0#, 0.0%
    output -- CF: True
    output -- time: 0.7s (0:00:00.711603)
    flips -- #0->1: 282
    flips -- #1->0: 1
    flips -- #NA->0: 185
    flips -- #NA->1: 560
    rates -- FN: 0.263
    rates -- FP: 0.00186567
    rates -- NA: 0.317
    score -- NLL: 637.364776250779




.. GENERATED FROM PYTHON SOURCE LINES 29-30

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

.. GENERATED FROM PYTHON SOURCE LINES 30-32

.. code-block:: Python

    tree = scp.ul.to_tree(df_out)








.. GENERATED FROM PYTHON SOURCE LINES 33-34

Finally we can draw the tree in `dendrogram` format.

.. GENERATED FROM PYTHON SOURCE LINES 34-51

.. code-block:: Python


    # scp.pl.dendro_tree(
    #     tree,
    #     cell_info=adata.obs,
    #     label_color="subclone_color",
    #     width=1200,
    #     height=600,
    #     dpi=200,
    #     distance_labels_to_bottom=3,
    #     inner_node_type="both",
    #     inner_node_size=2,
    #     annotation=[
    #         ("bar", "Axl", "Erbb3", 0.2),
    #         ("bar", "Mitf", "Mitf", 0.2),
    #     ],
    # )
    # TODO: fix








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

   **Total running time of the script:** (0 minutes 1.313 seconds)

**Estimated memory usage:**  10 MB


.. _sphx_glr_download_auto_examples_visualization_plot_dendrogram.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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