Epithelium Visualization¶

[1]:

import tyssue

import numpy as np
import pandas as pd

import matplotlib.pylab as plt
%matplotlib inline
import ipyvolume as ipv


from tyssue import Sheet, SheetGeometry  as geom
from tyssue.generation import three_faces_sheet
from tyssue.draw import sheet_view
from tyssue import config
from tyssue import Monolayer, config
from tyssue.generation import extrude

[2]:

datasets, specs = three_faces_sheet()
sheet = Sheet('3cells_2D', datasets, specs)


geom.update_all(sheet)

[3]:

sheet.vert_df.describe().head(3)

[3]:

	x	y	z	is_active	rho	height	basal_shift
count	13.000000	1.300000e+01	13.0	13.0	13.0	13.0	13.0
mean	0.000000	-8.540177e-18	0.0	1.0	0.0	-4.0	4.0
std	1.172604	1.172570e+00	0.0	0.0	0.0	0.0	0.0

Matplotlib based representation¶

Custom settings¶

These might go in a config file latter on.

Ploting itself¶

Epithelial sheet representation¶

The default¶

[4]:

draw_specs = tyssue.config.draw.sheet_spec()

[5]:

fig, ax = sheet_view(sheet, ['x', 'y'])


ax.set_xlim(-3, 2.5)
ax.set_ylim(-2.75, 2.75)
fig.set_size_inches((8, 8))

../_images/notebooks_Visualization_8_0.png

Coloring¶

[6]:

## Let's add a column to sheet.vert_df
sheet.vert_df['rand'] = np.linspace(0.0, 1.0, num=sheet.vert_df.shape[0])

cmap = plt.cm.get_cmap('viridis')
color_cmap = cmap(sheet.vert_df.rand)
draw_specs['vert']['visible'] = True

draw_specs['vert']['color'] = color_cmap
draw_specs['vert']['alpha'] = 0.5
draw_specs['vert']['s'] = 500

[7]:

coords = ['x', 'y']
fig, ax = sheet_view(sheet, coords, **draw_specs)

ax.set_xlim(-3, 2.5)
ax.set_ylim(-2.75, 2.75)
fig.set_size_inches((8, 8))

../_images/notebooks_Visualization_11_0.png

Filling the cells¶

[8]:

sheet.face_df['col'] = np.linspace(0.0, 1.0,
                                    num=sheet.face_df.shape[0])

cmap = plt.cm.get_cmap('viridis')
color_cmap = cmap(sheet.face_df.col)

draw_specs['edge']['visible'] = False

draw_specs['face']['visible'] = True
draw_specs['face']['color'] = sheet.face_df['col']
draw_specs['face']['alpha'] = 0.5


fig, ax = sheet_view(sheet, coords, **draw_specs)

../_images/notebooks_Visualization_13_0.png

[9]:

draw_specs['edge']['visible'] = True

#draw_specs['face']['visible'] = False
draw_specs['face']['color'] = color_cmap
draw_specs['face']['alpha'] = 0.5

edge_color = np.linspace(0.0, 1.0,
                        num=sheet.edge_df.shape[0])

cmap = plt.cm.get_cmap('viridis')
edge_cmap = cmap(edge_color)
draw_specs['edge']['color'] = edge_cmap #[0, 0, 0, 1]
#draw_specs['edge']['color'] = [0, 0, 0, 0.2]

draw_specs['edge']['width'] = 8. * np.linspace(0.0, 1.0,
                        num=sheet.edge_df.shape[0])

[10]:

fig, ax = sheet_view(sheet, coords, **draw_specs)

../_images/notebooks_Visualization_15_0.png

Ipyvolume based¶

[11]:

extruded = extrude(sheet.datasets, method='translation')
specs = config.geometry.bulk_spec()
monolayer = Monolayer('mono', extruded, specs)



ipv.clear()
fig2, mesh = sheet_view(monolayer, mode="3D")
fig2

Vertex based color¶

[12]:

color = (monolayer.vert_df.x**2
         + monolayer.vert_df.y**2
         + monolayer.vert_df.z**2)


ipv.clear()
fig2, mesh = sheet_view(monolayer, edge={"color":color}, mode="3D")
fig2

Edge based color¶

[13]:

color = monolayer.edge_df['dy']
ipv.clear()
fig2, mesh = sheet_view(monolayer, edge={"color":color}, mode="3D")
fig2

### Displaying faces

[14]:

draw_specs = config.draw.sheet_spec()

draw_specs['face']['visible'] = True

#draw_specs['face']['visible'] = False
draw_specs['face']['color'] = np.random.random(monolayer.face_df.shape[0])

draw_specs['face']['alpha'] = 0.5

ipv.clear()
fig2, mesh = sheet_view(monolayer, mode="3D", **draw_specs)
fig2

### Higlighting faces

[15]:

from tyssue.draw import highlight_cells, highlight_faces

[16]:

highlight_faces(monolayer.face_df, [0, 2, 3], reset_visible=True)

ipv.clear()
fig2, mesh = sheet_view(monolayer, mode="3D", **draw_specs)
fig2

[17]:

highlight_cells(monolayer, 1, reset_visible=True)

ipv.clear()
fig2, mesh = sheet_view(monolayer, mode="3D", **draw_specs)
fig2

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