Mouse Embryo Map

This example shows how to enhance a mouse embryo map.

Load dataset and prepare data

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

Here we have a predefined colormap for each cell type.

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()
points = ax.scatter(embryo['cell_x'], embryo['cell_y'], s=1, c=embryo['colors'])
points.set_rasterized(True)
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=10)

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)

if '__file__' in globals():
    from pathlib import Path
    import matplotlib.pyplot as plt

    plt.rcParams['svg.fonttype'] = 'none'
    save_path = Path(__file__).parent / "imgs"
    plt.savefig(save_path / "mouse_embryo.svg", bbox_inches="tight")
    plt.savefig(save_path / "mouse_embryo.png", dpi=300, bbox_inches="tight")