.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/plot_pbmc3k.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_plot_pbmc3k.py>`
        to download the full example code

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

.. _sphx_glr_auto_examples_plot_pbmc3k.py:


Visualizing Single-cell RNA-seq Data
====================================

.. GENERATED FROM PYTHON SOURCE LINES 6-58



.. image-sg:: /auto_examples/images/sphx_glr_plot_pbmc3k_001.png
   :alt: plot pbmc3k
   :srcset: /auto_examples/images/sphx_glr_plot_pbmc3k_001.png, /auto_examples/images/sphx_glr_plot_pbmc3k_001_2_00x.png 2.00x
   :class: sphx-glr-single-img





.. code-block:: Python


    import matplotlib as mpl
    import matplotlib.pyplot as plt
    from matplotlib.colors import Normalize
    import marsilea as ma
    import marsilea.plotter as mp

    from sklearn.preprocessing import normalize

    mpl.rcParams['font.size'] = 8

    pbmc3k = ma.load_data("pbmc3k")
    exp = pbmc3k['exp']
    pct_cells = pbmc3k['pct_cells']
    count = pbmc3k['count']

    matrix = normalize(exp.to_numpy(), axis=0)

    cell_cat = ['Lymphoid', 'Myeloid', 'Lymphoid', 'Lymphoid',
                'Lymphoid', 'Myeloid', 'Myeloid', 'Myeloid']

    # Make plots
    cells_proportion = mp.SizedMesh(
        pct_cells, size_norm=Normalize(vmin=0, vmax=100),
        color="none", edgecolor="#6E75A4",
        size_legend_kws=dict(title="% of cells", show_at=[.3, .5, .8, 1])
    )
    mark_high = mp.MarkerMesh(matrix > 0.7, color="#DB4D6D", label="High")
    cell_count = mp.Numbers(count['Value'], color="#fac858", label="Cell Count")
    cell_exp = mp.Violin(exp, label="Expression", linewidth=0, color="#ee6666")
    cell_types = mp.Labels(exp.index, align="center")
    gene_names = mp.Labels(exp.columns)

    # Group plots together
    h = ma.Heatmap(matrix, cmap="Greens", label="Normalized\nExpression",
                   width=3, height=3.5)
    h.add_layer(cells_proportion)
    h.add_layer(mark_high)
    h.add_right(cell_count, pad=.1, size=.7)
    h.add_top(cell_exp, pad=.1, size=.75)
    h.add_left(cell_types)
    h.add_bottom(gene_names)

    h.hsplit(labels=cell_cat, order=['Lymphoid', 'Myeloid'])
    h.add_left(mp.Chunk(['Lymphoid', 'Myeloid'], ["#33A6B8", "#B481BB"]),
               pad=.05)
    h.add_dendrogram("left", colors=["#33A6B8", "#B481BB"])
    h.add_dendrogram("bottom")
    h.add_legends(pad=.1)
    h.set_margin(.2)
    h.render()
    plt.show()


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

   **Total running time of the script:** (0 minutes 2.594 seconds)


.. _sphx_glr_download_auto_examples_plot_pbmc3k.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: plot_pbmc3k.ipynb <plot_pbmc3k.ipynb>`

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

      :download:`Download Python source code: plot_pbmc3k.py <plot_pbmc3k.py>`


.. only:: html

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

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