tyssue.draw package

Submodules

tyssue.draw.ipv_draw module

3D visualisation inside the notebook.

tyssue.draw.ipv_draw.browse_history(history, coords=['x', 'y', 'z'], **draw_specs_kw)

tyssue.draw.ipv_draw.edge_mesh(sheet, coords, **edge_specs)

Creates a ipyvolume Mesh of the edge lines to be displayed in Jupyter Notebooks

Returns

mesh

Return type

a ipyvolume.widgets.Mesh mesh widget

tyssue.draw.ipv_draw.face_mesh(sheet, coords, **face_draw_specs)

Creates a ipyvolume Mesh of the face polygons

tyssue.draw.ipv_draw.sheet_view(sheet, coords=['x', 'y', 'z'], **draw_specs_kw)

Creates a javascript renderer of the edge lines to be displayed in Jupyter Notebooks

Returns

• fig (a ipyvolume.widgets.Figure widget)

• mesh (a ipyvolume.widgets.Mesh mesh widget)

tyssue.draw.ipv_draw.update_view(fig, meshes)

tyssue.draw.ipv_draw.view_ipv(sheet, coords=['x', 'y', 'z'], **edge_specs)

Creates a javascript renderer of the edge lines to be displayed in Jupyter Notebooks

Returns

• fig (a ipyvolume.widgets.Figure widget)

• mesh (a ipyvolume.widgets.Mesh mesh widget)

tyssue.draw.plt_draw module

Matplotlib based plotting

tyssue.draw.plt_draw.create_gif(history, output, num_frames=60, draw_func=None, margin=5, **draw_kwds)

Creates an animated gif of the recorded history.

You need imagemagick on your system for this function to work.

Parameters

• history (a tyssue.History object) –

• output (path to the output gif file) –

• num_frames (int, the number of frames in the gif) –

• draw_func (a drawing function) – this function must take a sheet object as first argument and return a fig, ax pair. Defaults to quick_edge_draw (aka sheet_view with quick mode)

• margin (int, the graph margins in percents, default 5) – if margin is -1, let the draw function decide

• are passed to the drawing function (**draw_kwds) –

tyssue.draw.plt_draw.curved_view(sheet, radius_cutoff=1000.0)

tyssue.draw.plt_draw.draw_edge(sheet, coords, ax, **draw_spec_kw)

tyssue.draw.plt_draw.draw_face(sheet, coords, ax, **draw_spec_kw)

Draws epithelial sheet polygonal faces in matplotlib Keyword values can be specified at the element level as columns of the sheet.face_df

tyssue.draw.plt_draw.draw_vert(sheet, coords, ax, **draw_spec_kw)

Draw junction vertices in matplotlib

tyssue.draw.plt_draw.get_arc_data(sheet)

tyssue.draw.plt_draw.parse_face_specs(face_draw_specs, sheet)

tyssue.draw.plt_draw.plot_forces(sheet, geom, model, coords, scaling, ax=None, approx_grad=None, **draw_specs_kw)

Plot the net forces at each vertex, with their amplitudes multiplied by scaling. To be clear, this is the oposite of the gradient - grad E.

tyssue.draw.plt_draw.plot_junction(eptm, edge_index, coords=['x', 'y'])

Plots local graph around a junction, for debugging purposes

tyssue.draw.plt_draw.plot_scaled_energies(sheet, geom, model, scales, ax=None)

Plot scaled energies

Parameters

• sheet (a:class: Sheet object) –

• geom (a Geometry class) –

• model (a :class:'Model') –

• scales (np.linspace of float) –

Returns

• fig (a :class:matplotlib.figure.Figure instance)

• ax (:class:matplotlib.Axes instance, default None)

tyssue.draw.plt_draw.quick_edge_draw(sheet, coords=['x', 'y'], ax=None, **draw_spec_kw)

tyssue.draw.plt_draw.sheet_view(sheet, coords=['x', 'y'], ax=None, **draw_specs_kw)

Base view function, parametrizable through draw_secs

The default sheet_spec specification is:

{‘edge’: {

‘visible’: True, ‘width’: 0.5, ‘head_width’: 0.2, # arrow head width for the edges ‘length_includes_head’: True, # see matplotlib Arrow artist doc ‘shape’: ‘right’, ‘color’: ‘#2b5d0a’, # can be an array ‘alpha’: 0.8, ‘zorder’: 1, ‘colormap’: ‘viridis’},

‘vert’: {

‘visible’: True, ‘s’: 100, ‘color’: ‘#000a4b’, ‘alpha’: 0.3, ‘zorder’: 2},

‘face’: {

‘visible’: False, ‘color’: ‘#8aa678’, ‘alpha’: 1.0, ‘zorder’: -1} }

Module contents

tyssue.draw.highlight_cells(eptm, cells, reset_visible=False)

Sets a column ‘visible’ to True for all the faces of the cells passed as argument (for a 3D tyssue).

If no such column exists in eptm.face_df, creates it.

tyssue.draw.highlight_faces(face_df, faces, reset_visible=False)

Sets the faces visibility to 1

If reset_visible is True, sets all the other faces to visible = False

tyssue.draw.sheet_view(sheet, coords=['x', 'y', 'z'], ax=None, mode='2D', **draw_specs_kw)

Main plotting function in 2D or 3D.

Parameters

• sheet (Epithelium instance) –

• coords (list of strings,) – the coordinates over which to do the plot

• ax (:class:matplotlib.Axes instance, default None) – axis over which to plot the sheet, for quick and

• mode (str, {'2D'|'quick'|'3D'|'vispy'}, default '2D') – the type of graph to plot (see bellow)

Returns

Return type

fig, {ax|meshes}