def print_tensions(exp_organo, th_organo, to_save=False, path=None):
"""Print the tensions of an experimental organoid and the theoritical
organoid on the same plot and save it in a PNG image.
Parameters
----------
exp_organo : class AnnularSheet
the experimental organoid whose tensions will be ploted
th_organo : class AnnularSheet
the theoritical organoid which will be ploted behind exp_organo tensions
to_save : bool
if True the plot must be saved
path : string
path to the saved image.
Returns
----------
"""
draw_specs = sheet_spec()
tension_max = np.max(exp_organo.edge_df.line_tension.values.copy())
edge_color = 1/tension_max*exp_organo.edge_df.line_tension.values.copy()
cmap = plt.cm.get_cmap('viridis')
edge_cmap = cmap(edge_color)
draw_specs['vert']['visible'] = False
draw_specs['edge']['color'] = edge_cmap
draw_specs['edge']['width'] = 0.25+3*edge_color
fig, ax = quick_edge_draw(th_organo, lw=5, c='k', alpha=0.2)
fig, ax = sheet_view(exp_organo, ax=ax, **draw_specs)
fig.set_size_inches(12, 12)
plt.xlabel('Size in µm')
plt.ylabel('Size in µm')
if to_save:
plt.savefig(path)
def three_axis_sheet_view(sheet, face_mask=None):
"""
plot 3 view of the sheet :
* ventral view
* sagittal view
* lateral view
Parameters
----------
sheet : a :class:`tyssue.sheet` object
face_mask : string
"""
if face_mask is not None:
sheet_mesoderm = sheet.extract(face_mask)
else:
sheet_mesoderm = sheet
edge_specs = {'alpha': 0.6,
'lw': 0.1,
'color': 'black'}
scatter_specs = {'alpha': 0.8,
'ms': 5,
'color': 'red'}
plt.figure(figsize=(18.5, 10.5))
grid = gridspec.GridSpec(2, 2)
axes_1 = plt.subplot(grid[0, 0])
axes_2 = plt.subplot(grid[1, 0])
axes_3 = plt.subplot(grid[:, 1])
coord_pairs = [('z', 'y'), ('z', 'x'), ('x', 'y')]
titles = ['lateral view', 'ventral view', 'sagittal view']
axes = [axes_1, axes_2, axes_3]
for coords, title, ax in zip(coord_pairs, titles, axes):
u, v = coords
fig, ax = quick_edge_draw(sheet,
coords=coords,
ax=ax,
**edge_specs)
ax.plot(sheet_mesoderm.face_df[u],
sheet_mesoderm.face_df[v],
'o', **scatter_specs)
ax.set_title(title)
ax.set_xlabel(u)
ax.set_ylabel(v)
return fig, axes
def print_tensions(exp_organo, th_organo):
draw_specs = sheet_spec()
tension_max = np.max(exp_organo.edge_df.line_tension.values.copy())
edge_color = 1 / tension_max * exp_organo.edge_df.line_tension.values.copy(
)
cmap = plt.cm.get_cmap('viridis')
edge_cmap = cmap(edge_color)
draw_specs['vert']['visible'] = False
draw_specs['edge']['color'] = edge_cmap
draw_specs['edge']['width'] = 0.25 + 3 * edge_color
fig, ax = quick_edge_draw(th_organo, lw=5, c='k', alpha=0.2)
fig, ax = sheet_view(exp_organo, ax=ax, **draw_specs)
fig.set_size_inches(12, 12)
plt.xlabel('Size in µm')
plt.ylabel('Size in µm')
def mesoderm_position(sheet, mesoderm_cells):
"""
Plot two pannel view of the sheet and
the position of the mesoderm cells
"""
fig, axes = plt.subplots(1, 2, sharey=True)
fig, ax = quick_edge_draw(sheet, ['z', 'x'],
ax=axes[0],
alpha=0.7)
ax.plot(sheet.face_df.loc[mesoderm_cells, 'z'],
sheet.face_df.loc[mesoderm_cells, 'x'],
'o', alpha=0.8, ms=5)
fig, ax = quick_edge_draw(sheet, ['y', 'x'],
ax=axes[1],
alpha=0.7)
ax.plot(sheet.face_df.loc[mesoderm_cells, 'y'],
sheet.face_df.loc[mesoderm_cells, 'x'],
'o', alpha=0.8, ms=5)
fig.set_size_inches(24, 6)
return fig, axes
def test_quick_edge_draw(self):
fig, ax = quick_edge_draw(self.sheet)
assert ax.lines[0].get_xydata().shape == (54, 2)
def test_quick_edge_draw():
sheet = Sheet("test", *three_faces_sheet())
fig, ax = quick_edge_draw(sheet)
assert ax.lines[0].get_xydata().shape == (54, 2)