:orphan:

Examples
========

This section contains various code snippets that demonstrate :mod:`scphylo`'s
usage.



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Reconstruction
^^^^^^^^^^^^^^

Below is a gallery of examples for reconstructing tumor phylogeny using available tools
in :mod:`scphylo.tl`.



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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using PhISCS-BnB on a binary single-cell genotype matrix.">

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  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_bnb_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_bnb`

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      <div class="sphx-glr-thumbnail-title">Reconstruct tree by PhISCS-BnB</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using Trisicell-Boost on a binary single-cell genotype matrix.">

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  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_booster_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_booster`

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      <div class="sphx-glr-thumbnail-title">Reconstruct tree by Trisicell-Boost</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using gpps on a binary single-cell genotype matrix.">

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  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_gpps_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_gpps`

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      <div class="sphx-glr-thumbnail-title">Reconstruct tree by gpps</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using OncoNEM on a binary single-cell genotype matrix.">

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  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_onconem_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_onconem`

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      <div class="sphx-glr-thumbnail-title">Reconstruct tree by OncoNEM</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using PhISCS on a binary single-cell genotype matrix.">

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  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_phiscs_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_phiscs`

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      <div class="sphx-glr-thumbnail-title">Reconstruct tree by PhISCS</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using ScisTree on a binary single-cell genotype matrix.">

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  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_scistree_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_scistree`

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      <div class="sphx-glr-thumbnail-title">Reconstruct tree by ScisTree</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using SCITE on a binary single-cell genotype matrix.">

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  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_scite_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_scite`

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      <div class="sphx-glr-thumbnail-title">Reconstruct tree by SCITE</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using SiCloneFit on a binary single-cell genotype matrix.">

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  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_siclonefit_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_siclonefit`

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      <div class="sphx-glr-thumbnail-title">Reconstruct tree by SiCloneFit</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to construct a phylogenetic tree using SPhyR on a binary single-cell genotype matrix.">

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  .. image:: /auto_examples/reconstruction/images/thumb/sphx_glr_compute_sphyr_thumb.png
    :alt:

  :doc:`/auto_examples/reconstruction/compute_sphyr`

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      <div class="sphx-glr-thumbnail-title">Reconstruct tree by SPhyR</div>
    </div>


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    </div>

Comparison
^^^^^^^^^^

Below is a gallery of examples for comparing two phylogenetic trees using available
tools in :mod:`scphylo.tl`.



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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to compare/measure two inferred genotype data (trees).">

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  .. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_ad_thumb.png
    :alt:

  :doc:`/auto_examples/comparison/compute_ad`

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      <div class="sphx-glr-thumbnail-title">Comparing two trees by Ancestor-Descendent</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to compare/measure two inferred genotype data (trees).">

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  .. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_caset_thumb.png
    :alt:

  :doc:`/auto_examples/comparison/compute_caset`

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      <div class="sphx-glr-thumbnail-title">Comparing two trees by CASet</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to compare/measure two inferred genotype data (trees).">

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  .. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_disc_thumb.png
    :alt:

  :doc:`/auto_examples/comparison/compute_disc`

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      <div class="sphx-glr-thumbnail-title">Comparing two trees by DISC</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to compare/measure two inferred genotype data (trees).">

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  .. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_dl_thumb.png
    :alt:

  :doc:`/auto_examples/comparison/compute_dl`

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      <div class="sphx-glr-thumbnail-title">Comparing two trees by Different-Lineage</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to compare/measure two inferred genotype data (trees).">

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  .. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_gs_thumb.png
    :alt:

  :doc:`/auto_examples/comparison/compute_gs`

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      <div class="sphx-glr-thumbnail-title">Comparing two trees by Genotype-Similarity</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to compare/measure two inferred genotype data (trees).">

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  .. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_mltd_thumb.png
    :alt:

  :doc:`/auto_examples/comparison/compute_mltd`

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      <div class="sphx-glr-thumbnail-title">Comparing two trees by MLTD</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to compare/measure two inferred genotype data (trees).">

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  .. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_mp3_thumb.png
    :alt:

  :doc:`/auto_examples/comparison/compute_mp3`

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      <div class="sphx-glr-thumbnail-title">Comparing two trees by MP3</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to compare/measure two inferred genotype data (trees).">

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  .. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_rf_thumb.png
    :alt:

  :doc:`/auto_examples/comparison/compute_rf`

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      <div class="sphx-glr-thumbnail-title">Comparing two trees by Robinson-Foulds</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to compare/measure two inferred genotype data (trees).">

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  .. image:: /auto_examples/comparison/images/thumb/sphx_glr_compute_tpted_thumb.png
    :alt:

  :doc:`/auto_examples/comparison/compute_tpted`

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      <div class="sphx-glr-thumbnail-title">Comparing two trees by TPTED</div>
    </div>


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Assessment
^^^^^^^^^^

Below is a gallery of examples for assessing the inferred phylogenetic tree using
functions in :mod:`scphylo.tl`.



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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to assess a phylogenetic tree using Trisicell-PartF on a binary single-cell genotype matrix.">

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  .. image:: /auto_examples/assessment/images/thumb/sphx_glr_compute_partf_thumb.png
    :alt:

  :doc:`/auto_examples/assessment/compute_partf`

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      <div class="sphx-glr-thumbnail-title">Reconstruct tree by Trisicell-PartF</div>
    </div>


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    </div>

Visualization
^^^^^^^^^^^^^

Below is a gallery of examples for visualizing the inferred phylogenetic tree using
functions in :mod:`scphylo.pl`.



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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to visualize an inferred tree.">

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  .. image:: /auto_examples/visualization/images/thumb/sphx_glr_plot_clonal_thumb.png
    :alt:

  :doc:`/auto_examples/visualization/plot_clonal`

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      <div class="sphx-glr-thumbnail-title">Visualizing a tree in clonal format</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example shows how to visualize an inferred tree.">

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  .. image:: /auto_examples/visualization/images/thumb/sphx_glr_plot_dendrogram_thumb.png
    :alt:

  :doc:`/auto_examples/visualization/plot_dendrogram`

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      <div class="sphx-glr-thumbnail-title">Visualizing a tree in dendrogram format</div>
    </div>


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    </div>


.. toctree::
   :hidden:
   :includehidden:


   /auto_examples/reconstruction/index.rst
   /auto_examples/comparison/index.rst
   /auto_examples/assessment/index.rst
   /auto_examples/visualization/index.rst



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