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

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

.. _sphx_glr_auto_examples_plot_mouse_embryo.py:


Mouse Embryo Map
================

This example shows how to enhance a mouse embryo map.

.. GENERATED FROM PYTHON SOURCE LINES 10-12

Load dataset and prepare data
-----------------------------

.. GENERATED FROM PYTHON SOURCE LINES 12-38

.. code-block:: Python


    import numpy as np
    from matplotlib.colors import LinearSegmentedColormap
    from legendkit import cat_legend
    import marsilea as ma
    embryo = ma.load_data('mouse_embryo')

    xmax = embryo['cell_x'].max()
    ymax = embryo['cell_y'].max()
    xstart, xend = -xmax*0.05, xmax*1.05
    ystart, yend = -ymax*0.05, ymax*1.05

    xrange = np.linspace(xstart, xend, 200)
    yrange = np.linspace(ystart, yend, 200)

    xmid = (xrange[1:] + xrange[:-1]) / 2
    ymid = (yrange[1:] + yrange[:-1]) / 2


    def get_xy_hist(ct):
        x = embryo[embryo['cell_type'] == ct]['cell_x'].to_numpy()
        y = embryo[embryo['cell_type'] == ct]['cell_y'].to_numpy()
        xhist, _ = np.histogram(x, bins=xrange)
        yhist, _ = np.histogram(y, bins=yrange)
        return xhist, yhist








.. GENERATED FROM PYTHON SOURCE LINES 39-40

Here we have a predefined colormap for each cell type.

.. GENERATED FROM PYTHON SOURCE LINES 40-102

.. code-block:: Python


    colormap = {
        'Cavity': '#6d32e6',
        'Brain': '#bf024f',
        'Meninges': '#d147a3',
        'Choroid plexus': '#b3a726',
        'Cartilage primordium': '#103a14',
        'Jaw and tooth': '#ef833a',
        'Connective tissue': '#b38b5c',
        'Epidermis': '#35586d',
        'Lung primordium': '#3cb44b',
        'Sympathetic nerve': '#dfdce0',
        'Liver': '#bd3add',
        'Mucosal epithelium': '#0bd3b1',
        'GI tract': '#ff4374',
        'Mesentery': '#b74c11',
        'Dorsal root ganglion': '#036df4',
        'Muscle': '#dd7936',
        'Mesothelium': '#5c5ca6',
        'Blood vessel': '#be9b72',
        'Urogenital ridge': '#d3245a',
        'Heart': '#03fff4',
        'Pancreas': '#f062f9',
        'Kidney': '#62cfe8',
        'Ovary': '#c923b1'
    }


    width = 5
    height = width * (yend - ystart) / (xend - xstart)
    b = ma.WhiteBoard(height=height, width=width)

    cell_types = ["Brain", "Cartilage primordium", "Liver", "Heart", "GI tract"]
    for n in cell_types:
        b.add_canvas("bottom", size=.2, pad=.1, name=f"{n}-x")
        b.add_canvas("right", size=.2, pad=.1, name=f"{n}-y")
    b.render()

    # Draw cell
    ax = b.get_main_ax()
    ax.scatter(embryo['cell_x'], embryo['cell_y'], s=1, c=embryo['colors'])
    ax.set_xlim(xstart, xend)
    ax.set_ylim(ystart, yend)
    ax.set_title("Mouse Embryo E12.5")
    ax.set_axis_off()

    colors = list(colormap.values())
    labels = list(colormap.keys())
    cat_legend(colors=colors, labels=labels, ax=ax, loc="out left center", fontsize=8)

    for n in cell_types:
        xh, yh = get_xy_hist(n)
        cmap = LinearSegmentedColormap.from_list(n, ["white", colormap[n]])
        x_ax = b.get_ax(f"{n}-x")
        x_ax.pcolormesh(xh.reshape(1, -1), cmap=cmap)
        x_ax.set_axis_off()
        x_ax.text(0, .5, n, va="center", ha="right", transform=x_ax.transAxes)

        y_ax = b.get_ax(f"{n}-y")
        y_ax.pcolormesh(yh.reshape(-1, 1), cmap=cmap)
        y_ax.set_axis_off()
        y_ax.text(0.5, 0, n, va="top", ha="center", rotation=90, transform=y_ax.transAxes)



.. image-sg:: /auto_examples/images/sphx_glr_plot_mouse_embryo_001.png
   :alt: Mouse Embryo E12.5
   :srcset: /auto_examples/images/sphx_glr_plot_mouse_embryo_001.png, /auto_examples/images/sphx_glr_plot_mouse_embryo_001_2_00x.png 2.00x
   :class: sphx-glr-single-img






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

   **Total running time of the script:** (0 minutes 3.582 seconds)


.. _sphx_glr_download_auto_examples_plot_mouse_embryo.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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