`spateo.plotting.static.three_d_plot`#

Submodules#

Package Contents#

Functions#

`deformation`(*adata, deformed_grid[, layer, group_key, ...])
`multi_models`(*adata[, layer, group_key, spatial_key, ...])	Visualize multiple models separately in one figure.
`backbone`(backbone_model[, backbone_key, ...])	Visualize constructed 3D backbone model.
`acceleration`(adata, model[, acceleration_key, ...])	Visualize the torsion result.
`curl`(adata, model[, curl_key, filename, jupyter, ...])	Visualize the curl result.
`curvature`(adata, model[, curvature_key, filename, ...])	Visualize the curvature result.
`divergence`(adata, model[, divergence_key, filename, ...])	Visualize the divergence result.
`jacobian`(adata, model[, jacobian_key, filename, ...])	Visualize the jacobian result.
`torsion`(adata, model[, torsion_key, filename, ...])	Visualize the torsion result.
`pairwise_iteration`(adataA, adataB[, layer, group_key, ...])	Visualize the results of each iteration in the alignment process.
`pairwise_mapping`([idA, idB, adataA, adataB, pi, ...])	Visualize the pairing of cells between two models.
`pi_heatmap`(pi[, model1_name, model2_name, colormap, ...])	Visualize a heatmap of the pi matrix.
`merge_animations`([mp4_files, mp4_folder, filename])	Use MoviePy to compose a new animation and play multiple animations together in the new animation.
`three_d_animate`(models[, stable_model, stable_kwargs, ...])	Animated visualization of 3D reconstruction model.
`three_d_multi_plot`(model[, key, filename, jupyter, ...])	Multi-view visualization of reconstructed 3D model.
`three_d_plot`(model[, key, filename, jupyter, ...])	Visualize reconstructed 3D model.

spateo.plotting.static.three_d_plot.deformation(*adata: anndata.AnnData, deformed_grid: pyvista.PolyData | List[pyvista.PolyData], layer: str = 'X', group_key: str | list = None, spatial_key: str = 'align_spatial', id_key: str = 'slices', deformation_key: str | None = 'deformation', center_zero: bool = False, show_model: bool = True, filename: str | None = None, jupyter: bool | Literal[none, static, trame] = False, off_screen: bool = False, cpo: str | list = 'xy', shape: str | list | tuple = None, window_size: tuple | None = (1024, 756), background: str = 'white', model_color: str | list = 'red', model_alpha: float | list | dict = 1, colormap: str | list | dict = 'black', alphamap: float | list | dict = 1.0, ambient: float | list = 0.2, opacity: float | numpy.ndarray | list = 1.0, grid_size: float | list = 2.0, model_size: float | list = 3.0, show_axes: bool = True, show_legend: bool = False, legend_kwargs: dict | None = None, text: bool | str = True, text_kwargs: dict | None = None, **kwargs)[source]#

Visualize multiple models separately in one figure.

Parameters:

*adata

A list of models[Anndata object].

layer

If 'X', uses .X, otherwise uses the representation given by .layers[layer].

group_key

The key that stores clustering or annotation information in .obs, a gene name or a list of gene names in .var.

spatial_key

The key in .obsm that corresponds to the spatial coordinate of each bucket.

id_key

The key in .obs that corresponds to the model id of each bucket.

mode

Three modes of visualization. Available mode are:

'single' - Visualize each model individually.
'overlap' - Simultaneously visualize two models aligned front to back in one subplot.
'both' - Simultaneously visualize both types above.

center_zero

Whether to move the center point of the model to the (0, 0, 0).

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'. When jupyter=False, if you want to save ‘.png’ file, please ensure off_screen=True.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'trame' - Show a trame widget
'static' - Display a static figure.

off_screen

Renders off-screen when True. Useful for automated screenshots.

cpo

Camera position of the active render window. Available cpo are:

Iterable containing position, focal_point, and view up.
E.g.: [(2.0, 5.0, 13.0), (0.0, 0.0, 0.0), (-0.7, -0.5, 0.3)].
Iterable containing a view vector.
E.g.: [-1.0, 2.0, -5.0].
A string containing the plane orthogonal to the view direction.
E.g.: 'xy', 'xz', 'yz', 'yx', 'zx', 'zy', 'iso'.

shape

Number of sub-render windows inside the main window. By default, there is only one render window.

Specify two across with ``shape``=(2, 1) and a two by two grid with ``shape``=(2, 2).
shape Can also accept a string descriptor as shape.

E.g.: shape="3|1" means 3 plots on the left and 1 on the right, E.g.: shape="4/2" means 4 plots on top and 2 at the bottom.

window_size

Window size in pixels. The default window_size is [512, 512].

background

The background color of the window.

colormap

Colors to use for plotting pc. The default colormap is 'dodgerblue'.

overlap_cmap

Colors to use for plotting overlapped pc. The default colormap is 'red'.

alphamap

The opacity of the colors to use for plotting pc. The default alphamap is 1.0.

overlap_amap

The opacity of the colors to use for plotting overlapped pc. The default alphamap is .5.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

opacity

Opacity of the model.

If a single float value is given, it will be the global opacity of the model and uniformly applied everywhere, elif a numpy.ndarray with single float values is given, it will be the opacity of each point. - should be between 0 and 1.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

model_size

The point size of any nodes in the dataset plotted.

show_axes

Whether to add a camera orientation widget to the active renderer.

show_legend

whether to add a legend to the plotter.

legend_kwargs

A dictionary that will be pass to the add_legend function.

By default, it is an empty dictionary and the add_legend function will use the {"legend_size": None, "legend_loc": None, "legend_size": None, "legend_loc": None, "title_font_size": None, "label_font_size": None, "font_family": "arial", "fmt": "%.2e", "n_labels": 5, "vertical": True} as its parameters. Otherwise, you can provide a dictionary that properly modify those keys according to your needs.

text

The text to add the rendering.

text_kwargs

A dictionary that will be pass to the add_text function.

By default, it is an empty dictionary and the add_legend function will use the { "font_family": "arial", "font_size": 12, "font_color": "black", "text_loc": "upper_left"} as its parameters. Otherwise, you can provide a dictionary that properly modify those keys according to your needs.

**kwargs

Additional parameters that will be passed to three_d_multi_plot function.

Visualize constructed 3D backbone model.

Parameters:

backbone_model

The constructed backbone model.

backbone_key

Any point_data names or cell_data names to be used for coloring backbone_model.

backbone_model_size

The thickness of backbone.

backbone_colormap

Name of the Matplotlib colormap to use when mapping the scalars of backbone_model.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

backbone_ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

backbone_opacity

Opacity of the model.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

nodes_key

The key that corresponds to the coordinates of the nodes in the backbone.

nodes_label_size

Sets the size of the title font.

bg_model

The background model used to construct backbone model.

bg_key

Any point_data names or cell_data names to be used for coloring bg_model.

bg_model_style

Visualization style of bg_model. One of the following:

bg_model_style = 'surface',
bg_model_style = 'wireframe',
bg_model_style = 'points'.

bg_model_size

If bg_model_style = 'points', point size of any nodes in the dataset plotted.

If bg_model_style = 'wireframe', thickness of lines.

bg_colormap

Name of the Matplotlib colormap to use when mapping the scalars of bg_model.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

bg_ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

bg_opacity

Opacity of the model.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

show_axes

Whether to add a camera orientation widget to the active renderer.

show_legend

whether to add a legend of bg_model to the plotter.

legend_kwargs

A dictionary that will be pass to the add_legend function. By default, it is an empty dictionary and the add_legend function will use the {"legend_size": None, "legend_loc": None, "legend_size": None, "legend_loc": None, "title_font_size": None, "label_font_size": None, "font_family": "arial", "fmt": "%.2e", "n_labels": 5, "vertical": True} as its parameters. Otherwise, you can provide a dictionary that properly modify those keys according to your needs.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'. When jupyter=False, if you want to save ‘.png’ file, please ensure off_screen=True.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'trame' - Show a trame widget
'static' - Display a static figure.

off_screen

Renders off-screen when True. Useful for automated screenshots.

window_size

Window size in pixels. The default window_size is [512, 512].

background

The background color of the window.

cpo

Camera position of the active render window. Available cpo are:

Iterable containing position, focal_point, and view up.
E.g.: [(2.0, 5.0, 13.0), (0.0, 0.0, 0.0), (-0.7, -0.5, 0.3)].
Iterable containing a view vector.
E.g.: [-1.0, 2.0, -5.0].
A string containing the plane orthogonal to the view direction.
E.g.: 'xy', 'xz', 'yz', 'yx', 'zx', 'zy', 'iso'.

**kwargs

Additional parameters that will be passed to .add_point_labels function.

Returns:

List of camera position, focal point, and view up.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.
img: Numpy array of the last image.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.

Return type:

cpo

Visualize the torsion result.

Parameters:

adata

An anndata object contain acceleration values in .obs[acceleration_key].

model

A reconstructed model contains obs_index values.

acceleration_key

The key in .obs that corresponds to the acceleration values in the anndata object.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'. When jupyter=False, if you want to save ‘.png’ file, please ensure off_screen=True.
Output a gif file, please enter a filename ending with .gif.
Output a mp4 file, please enter a filename ending with .mp4.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'trame' - Show a trame widget
'static' - Display a static figure.

colormap

Name of the Matplotlib colormap to use when mapping the scalars.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

opacity

Opacity of the model.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

model_style

Visualization style of the model. One of the following:

model_style = 'surface',
model_style = 'wireframe',
model_style = 'points'.

model_size

If model_style = 'points', point size of any nodes in the dataset plotted.

If model_style = 'wireframe', thickness of lines.

**kwargs

Additional parameters that will be passed into the st.pl.feature function.

Returns:

List of camera position, focal point, and view up.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.
img: Numpy array of the last image.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.

Return type:

cpo

Examples

Visualize only in one model:

st.pl.acceleration(: adata=stage_adata, model=stage_pc, acceleration_key=”acceleration”, jupyter=”static”, model_style=”points”, model_size=3

)

Visualize in multiple model:

st.pl.acceleration(: adata=stage_adata, model=[stage_pc, trajectory_model], acceleration_key=”acceleration”, jupyter=”static”, model_style=[“points”, “wireframe”], model_size=[3, 1]

)

Visualize the curl result.

Parameters:

adata

An anndata object contain curl values in .obs[curl_key].

model

A reconstructed model contains obs_index values.

curl_key

The key in .obs that corresponds to the curl values in the anndata object.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'. When jupyter=False, if you want to save ‘.png’ file, please ensure off_screen=True.
Output a gif file, please enter a filename ending with .gif.
Output a mp4 file, please enter a filename ending with .mp4.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'trame' - Show a trame widget
'static' - Display a static figure.

colormap

Name of the Matplotlib colormap to use when mapping the scalars.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

opacity

Opacity of the model.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

model_style

Visualization style of the model. One of the following:

model_style = 'surface',
model_style = 'wireframe',
model_style = 'points'.

model_size

If model_style = 'points', point size of any nodes in the dataset plotted.

If model_style = 'wireframe', thickness of lines.

**kwargs

Additional parameters that will be passed into the st.pl.feature function.

Returns:

List of camera position, focal point, and view up.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.
img: Numpy array of the last image.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.

Return type:

cpo

Examples

Visualize only in one model:

st.pl.curl(: adata=stage_adata, model=stage_pc, curl_key=”curl”, jupyter=”static”, model_style=”points”, model_size=3

)

Visualize in multiple model:

st.pl.curl(: adata=stage_adata, model=[stage_pc, trajectory_model], curl_key=”curl”, jupyter=”static”, model_style=[“points”, “wireframe”], model_size=[3, 1]

)

Visualize the curvature result.

Parameters:

adata

An anndata object contain curvature values in .obs[curvature_key].

model

A reconstructed model contains obs_index values.

curvature_key

The key in .obs that corresponds to the curvature values in the anndata object.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'. When jupyter=False, if you want to save ‘.png’ file, please ensure off_screen=True.
Output a gif file, please enter a filename ending with .gif.
Output a mp4 file, please enter a filename ending with .mp4.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'trame' - Show a trame widget
'static' - Display a static figure.

colormap

Name of the Matplotlib colormap to use when mapping the scalars.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

opacity

Opacity of the model.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

model_style

Visualization style of the model. One of the following:

model_style = 'surface',
model_style = 'wireframe',
model_style = 'points'.

model_size

If model_style = 'points', point size of any nodes in the dataset plotted.

If model_style = 'wireframe', thickness of lines.

**kwargs

Additional parameters that will be passed into the st.pl.feature function.

Returns:

List of camera position, focal point, and view up.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.
img: Numpy array of the last image.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.

Return type:

cpo

Examples

Visualize only in one model:

st.pl.curvature(: adata=stage_adata, model=stage_pc, curvature_key=”curvature”, jupyter=”static”, model_style=”points”, model_size=3

)

Visualize in multiple model:

st.pl.curvature(: adata=stage_adata, model=[stage_pc, trajectory_model], curvature_key=”curvature”, jupyter=”static”, model_style=[“points”, “wireframe”], model_size=[3, 1]

)

Visualize the divergence result.

Parameters:

adata

An anndata object contain curl values in .obs[divergence_key].

model

A reconstructed model contains obs_index values.

divergence_key

The key in .obs that corresponds to the divergence values in the anndata object.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'. When jupyter=False, if you want to save ‘.png’ file, please ensure off_screen=True.
Output a gif file, please enter a filename ending with .gif.
Output a mp4 file, please enter a filename ending with .mp4.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'pythreejs' - Show a pythreejs widget
'static' - Display a static figure.
'ipygany' - Show an ipygany widget
'panel' - Show a panel widget.

colormap

Name of the Matplotlib colormap to use when mapping the scalars.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

opacity

Opacity of the model.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

model_style

Visualization style of the model. One of the following:

model_style = 'surface',
model_style = 'wireframe',
model_style = 'points'.

model_size

If model_style = 'points', point size of any nodes in the dataset plotted.

If model_style = 'wireframe', thickness of lines.

**kwargs

Additional parameters that will be passed into the st.pl.feature function.

Returns:

List of camera position, focal point, and view up.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.
img: Numpy array of the last image.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.

Return type:

cpo

Examples

Visualize only in one model:

st.pl.divergence(: adata=stage_adata, model=stage_pc, divergence_key=”divergence”, jupyter=”static”, model_style=”points”, model_size=3

)

Visualize in multiple model:

st.pl.divergence(: adata=stage_adata, model=[stage_pc, trajectory_model], divergence_key=”divergence”, jupyter=”static”, model_style=[“points”, “wireframe”], model_size=[3, 1]

)

Visualize the jacobian result.

Parameters:

adata

An anndata object contain jacobian matrix in .uns[jacobian_key].

model

A reconstructed model contains obs_index values.

jacobian_key

The key in .uns that corresponds to the jacobian matrix in the anndata object.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'. When jupyter=False, if you want to save ‘.png’ file, please ensure off_screen=True.
Output a gif file, please enter a filename ending with .gif.
Output a mp4 file, please enter a filename ending with .mp4.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'trame' - Show a trame widget
'static' - Display a static figure.

off_screen

Renders off-screen when True. Useful for automated screenshots.

shape

Number of sub-render windows inside the main window. By default, there are nine render window.

Specify two across with ``shape``=(2, 1) and a two by two grid with ``shape``=(2, 2).
shape Can also accept a string descriptor as shape.

E.g.: shape="3|1" means 3 plots on the left and 1 on the right, E.g.: shape="4/2" means 4 plots on top and 2 at the bottom.

window_size

Window size in pixels. The default window_size is [512*3, 512*3].

background

The background color of the window.

colormap

Name of the Matplotlib colormap to use when mapping the scalars.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

opacity

Opacity of the model.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

model_style

Visualization style of the model. One of the following:

model_style = 'surface',
model_style = 'wireframe',
model_style = 'points'.

model_size

If model_style = 'points', point size of any nodes in the dataset plotted.

If model_style = 'wireframe', thickness of lines.

show_axes

Whether to add a camera orientation widget to the active renderer.

show_legend

whether to add a legend to the plotter.

legend_kwargs

text

The text to add the rendering.

text_kwargs

A dictionary that will be pass to the add_text function.

**kwargs

Additional parameters that will be passed into the st.pl.three_d_multi_plot function.

Returns:

List of camera position, focal point, and view up.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.
img: Numpy array of the last image.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.

Return type:

cpo

Examples

Visualize only in one model:

st.pl.jacobian(: adata=stage_adata, model=stage_pc, jacobian_key=”jacobian”, jupyter=”static”, model_style=”points”, model_size=3

)

Visualize in multiple model:

st.pl.jacobian(: adata=stage_adata, model=[stage_pc, trajectory_model], jacobian_key=”jacobian”, jupyter=”static”, model_style=[“points”, “wireframe”], model_size=[3, 1]

)

Visualize the torsion result.

Parameters:

adata

An anndata object contain torsion values in .obs[torsion_key].

model

A reconstructed model contains obs_index values.

torsion_key

The key in .obs that corresponds to the torsion values in the anndata object.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'. When jupyter=False, if you want to save ‘.png’ file, please ensure off_screen=True.
Output a gif file, please enter a filename ending with .gif.
Output a mp4 file, please enter a filename ending with .mp4.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'trame' - Show a trame widget
'static' - Display a static figure.

colormap

Name of the Matplotlib colormap to use when mapping the scalars.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

opacity

Opacity of the model.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

model_style

Visualization style of the model. One of the following:

model_style = 'surface',
model_style = 'wireframe',
model_style = 'points'.

model_size

If model_style = 'points', point size of any nodes in the dataset plotted.

If model_style = 'wireframe', thickness of lines.

**kwargs

Additional parameters that will be passed into the st.pl.feature function.

Returns:

List of camera position, focal point, and view up.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.
img: Numpy array of the last image.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.

Return type:

cpo

Examples

Visualize only in one model:

st.pl.torsion(: adata=stage_adata, model=stage_pc, torsion_key=”torsion”, jupyter=”static”, model_style=”points”, model_size=3

)

Visualize in multiple model:

st.pl.torsion(: adata=stage_adata, model=[stage_pc, trajectory_model], torsion_key=”torsion”, jupyter=”static”, model_style=[“points”, “wireframe”], model_size=[3, 1]

)

spateo.plotting.static.three_d_plot.pairwise_iteration(adataA: anndata.AnnData, adataB: anndata.AnnData, layer: str = 'X', group_key: str | list = None, spatial_key: str = 'align_spatial', iter_key: str = 'iter_spatial', id_key: str = 'slices', filename: str = 'animate.mp4', jupyter: bool | Literal[none, static, trame] = False, off_screen: bool = False, cpo: str | list | None = None, window_size: tuple | None = None, background: str = 'black', modelA_cmap: str = 'dodgerblue', modelB_cmap: str = 'red', ambient: int | float = 0.3, modelA_opacity: int | float = 0.8, modelB_opacity: int | float = 1.0, model_size: float | list = 6.0, show_axes: bool = True, show_legend: bool = True, legend_kwargs: dict | None = None, text: bool | str = True, text_kwargs: dict | None = None, framerate: int = 6, **kwargs)[source]#

Visualize the results of each iteration in the alignment process.

Parameters:

adataA

Anndata object of modelA.

adataB

Anndata object of modelB.

layer

If 'X', uses .X, otherwise uses the representation given by .layers[layer].

group_key

The key that stores clustering or annotation information in .obs, a gene name or a list of gene names in .var.

spatial_key

The key in .obsm that corresponds to the spatial coordinate of each bucket.

iter_key

The key in .uns that corresponds to the result of each iteration of the iterative process.

id_key

The key in .obs that corresponds to the model id of each bucket.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output a gif file, please enter a filename ending with .gif.
Output a mp4 file, please enter a filename ending with .mp4.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'trame' - Show a trame widget
'static' - Display a static figure.

off_screen

Renders off-screen when True. Useful for automated screenshots.

cpo

Camera position of the active render window. Available cpo are:

Iterable containing position, focal_point, and view up.
E.g.: [(2.0, 5.0, 13.0), (0.0, 0.0, 0.0), (-0.7, -0.5, 0.3)].
Iterable containing a view vector.
E.g.: [-1.0, 2.0, -5.0].
A string containing the plane orthogonal to the view direction.
E.g.: 'xy', 'xz', 'yz', 'yx', 'zx', 'zy', 'iso'.

window_size

Window size in pixels. The default window_size is [512, 512].

background

The background color of the window.

modelA_cmap

Colors to use for plotting modelA. The default colormap is 'dodgerblue'.

modelB_cmap

Colors to use for plotting modelB. The default colormap is 'red'.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

modelA_opacity

Opacity of the modelA.

modelB_opacity

Opacity of the modelB.

model_size

The point size of any nodes in the dataset plotted.

show_axes

Whether to add a camera orientation widget to the active renderer.

show_legend

whether to add a legend to the plotter.

legend_kwargs

A dictionary that will be pass to the add_legend function.

text

The text to add the rendering.

text_kwargs

A dictionary that will be pass to the add_text function.

framerate

Frames per second.

**kwargs

Additional parameters that will be passed to three_d_animate function.

spateo.plotting.static.three_d_plot.pairwise_mapping(idA: str = 'sampleA', idB: str = 'sampleB', adataA: anndata.AnnData | None = None, adataB: anndata.AnnData | None = None, pi: numpy.ndarray | None = None, modelA: pyvista.PolyData | None = None, modelB: pyvista.PolyData | None = None, model_lines: pyvista.PolyData | None = None, layer: str = 'X', group_key: str | list = None, spatial_key: str = 'align_spatial', keep_all: bool = False, distance: int | float | None = 300, direction: Literal[x, y, pairwise_mapping.z] | None = 'z', filename: str | None = None, jupyter: bool | Literal[none, static, trame] = False, off_screen: bool = False, cpo: str | list | None = 'iso', window_size: tuple | None = (1024, 1024), background: str = 'black', modelA_cmap: str = 'dodgerblue', modelA_amap: float | list = 1.0, modelB_cmap: str = 'red', modelB_amap: float | list = 1.0, line_color: str = 'gainsboro', line_alpha: float | list = 1.0, ambient: float = 0.3, model_opacity: float = 1, line_opacity: float = 0.03, model_size: float | list = 6.0, line_size: float | list = 2.0, show_axes: bool = True, show_legend: bool = True, legend_kwargs: dict | None = None, text: bool | str = True, text_kwargs: dict | None = None, **kwargs)[source]#

Visualize the pairing of cells between two models.

Parameters:

idA

ID of modelA.

idB

ID of modelB.

adataA

Anndata object of modelA.

adataB

Anndata object of modelB.

pi

The pi matrix obtained by alignment.

modelA

The point cloud model of adataA.

modelB

The point cloud model of adataB.

model_lines

Cell connection lines between modelA and modelB

layer

If 'X', uses .X, otherwise uses the representation given by .layers[layer].

group_key

The key that stores clustering or annotation information in .obs, a gene name or a list of gene names in .var.

spatial_key

The key in .obsm that corresponds to the spatial coordinate of each bucket.

keep_all

Whether to retain all the optimal relationships obtained only based on the pi matrix, If keep_all is False, the optimal relationships obtained based on the pi matrix and the nearest coordinates.

distance

Distance between modelA and modelB when visualizing.

direction

The direction between modelA and modelB when visualizing.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'. When jupyter=False, if you want to save ‘.png’ file, please ensure off_screen=True.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'trame' - Show a trame widget
'static' - Display a static figure.

off_screen

Renders off-screen when True. Useful for automated screenshots.

cpo

Camera position of the active render window. Available cpo are:

Iterable containing position, focal_point, and view up.
E.g.: [(2.0, 5.0, 13.0), (0.0, 0.0, 0.0), (-0.7, -0.5, 0.3)].
Iterable containing a view vector.
E.g.: [-1.0, 2.0, -5.0].
A string containing the plane orthogonal to the view direction.
E.g.: 'xy', 'xz', 'yz', 'yx', 'zx', 'zy', 'iso'.

window_size

Window size in pixels. The default window_size is (1024, 1024).

background

The background color of the window.

modelA_cmap

Colors to use for plotting modelA. The default colormap is 'dodgerblue'.

modelA_amap

The opacity of the colors to use for plotting modelA. The default alphamap is 1.0.

modelB_cmap

Colors to use for plotting modelB. The default colormap is 'red'.

modelB_amap

The opacity of the colors to use for plotting modelB. The default alphamap is 1.0.

line_color

Colors to use for plotting lines. The default colormap is 'gainsboro'.

line_alpha

Alpha to use for plotting lines. The default colormap is 'gainsboro'.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

model_opacity

Opacity of the modelA and modelB.

line_opacity

Opacity of the lines.

model_size

The point size of any nodes in the dataset plotted.

line_size

The line size of lines in the dataset plotted.

show_axes

Whether to add a camera orientation widget to the active renderer.

show_legend

whether to add a legend to the plotter.

legend_kwargs

A dictionary that will be pass to the add_legend function.

text

The text to add the rendering.

text_kwargs

A dictionary that will be pass to the add_text function.

**kwargs

Additional parameters that will be passed to three_d_plot function.

Returns:

The point cloud models of adataA. pcB: The point cloud models of adataB. model_lines: Cell mapping lines between modelA and modelB.

Return type:

pcA

spateo.plotting.static.three_d_plot.pi_heatmap(pi: numpy.ndarray, model1_name: str = 'model1', model2_name: str = 'model2', colormap: str = 'hot_r', fig_height: int | float = 3, robust: bool = False, vmin: int | float | None = None, vmax: int | float | None = None, fontsize: int | float = 12, filename: str | None = None, **kwargs)[source]#

Visualize a heatmap of the pi matrix.

Parameters:

pi: The pi matrix obtained by alignment.
model1_name: The name/id of model1.
model2_name: The name/id of model2.
colormap: Colors to use for plotting heatmap. The default colormap is 'hot_r'.
fig_height: Figure height.
robust: If True and vmin or vmax are absent, the colormap range is computed with robust quantiles instead of the extreme values.
vmin: Values to anchor the colormap, otherwise they are inferred from the data and other keyword arguments.
vmax: Values to anchor the colormap, otherwise they are inferred from the data and other keyword arguments.
fontsize: The font size of x label and y label.
filename: Filename of output file.
**kwargs: Additional parameters that will be passed to sns.heatmap function.

spateo.plotting.static.three_d_plot.merge_animations(mp4_files: list | None = None, mp4_folder: list | None = None, filename: str = 'merged_animation.mp4')[source]#

Use MoviePy to compose a new animation and play multiple animations together in the new animation.

Parameters:

mp4_files: A list containing absolute paths to mp4 files that need to be played together.
mp4_folder: Absolute path to the folder containing all mp4 files that need to be played together. If mp4_files is provided, mp4_folder cannot also be provided.
filename: Absolute path to save the newly composed animation.

Examples

st.pl.merge_animations(mp4_files=[“animation1.mp4”, “animation2.mp4”], filename=f”merged_animation.mp4”)

spateo.plotting.static.three_d_plot.three_d_animate(models: Union[List[PolyData or UnstructuredGrid], pyvista.MultiBlock], stable_model: pyvista.PolyData | pyvista.UnstructuredGrid | pyvista.MultiBlock | None = None, stable_kwargs: dict | None = None, key: str | None = None, filename: str = 'animate.mp4', jupyter: bool | Literal[panel, none, pythreejs, static, ipygany] = False, off_screen: bool = False, window_size: tuple = (512, 512), background: str = 'white', cpo: str | list = 'iso', colormap: str | list | None = None, ambient: float | list = 0.2, opacity: float | numpy.ndarray | list = 1.0, model_style: Literal[points, surface, wireframe] | list = 'surface', model_size: float | list = 3.0, show_legend: bool = True, legend_kwargs: dict | None = None, show_outline: bool = False, outline_kwargs: dict | None = None, text: str | None = None, text_kwargs: dict | None = None, framerate: int = 24, plotter_filename: str | None = None)[source]#

Animated visualization of 3D reconstruction model.

Parameters:

models

A List of reconstructed models or a MultiBlock.

stable_model

The model that do not change with time in animation.

stable_kwargs

Parameters for plotting stable model. Available stable_kwargs are:

'key'
'ambient'
'opacity'
'model_style'
'model_size'
'background'
'show_legend'
'legend_kwargs'
'show_outline'
'outline_kwargs'
'text'
'text_kwargs'

key

The key under which are the labels.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output a gif file, please enter a filename ending with .gif.
Output a mp4 file, please enter a filename ending with .mp4.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'pythreejs' - Show a pythreejs widget
'static' - Display a static figure.
'ipygany' - Show an ipygany widget
'panel' - Show a panel widget.

off_screen

Renders off-screen when True. Useful for automated screenshots.

window_size

Window size in pixels. The default window_size is [512, 512].

background

The background color of the window.

cpo

Camera position of the active render window. Available cpo are:

Iterable containing position, focal_point, and view up.
E.g.: [(2.0, 5.0, 13.0), (0.0, 0.0, 0.0), (-0.7, -0.5, 0.3)].
Iterable containing a view vector.
E.g.: [-1.0, 2.0, -5.0].
A string containing the plane orthogonal to the view direction.
E.g.: 'xy', 'xz', 'yz', 'yx', 'zx', 'zy', 'iso'.

colormap

Name of the Matplotlib colormap to use when mapping the scalars.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

opacity

Opacity of the model.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

model_style

Visualization style of the model. One of the following:

model_style = 'surface',
model_style = 'wireframe',
model_style = 'points'.

model_size

If model_style = 'points', point size of any nodes in the dataset plotted.

If model_style = 'wireframe', thickness of lines.

show_legend

whether to add a legend to the plotter.

legend_kwargs

show_outline

whether to produce an outline of the full extent for the model.

outline_kwargs

A dictionary that will be pass to the add_outline function.

By default, it is an empty dictionary and the add_legend function will use the {"outline_width": 5.0, "outline_color": "black", "show_labels": True, "font_size": 16, "font_color": "white", "font_family": "arial"} as its parameters. Otherwise, you can provide a dictionary that properly modify those keys according to your needs.

text

The text to add the rendering.

text_kwargs

A dictionary that will be pass to the add_text function.

framerate

Frames per second. Only available when filename ending with .mp4 or .gif.

plotter_filename

The filename of the file where the plotter is saved.: Writer type is inferred from the extension of the filename.

Output a gltf file, please enter a filename ending with .gltf.
Output a html file, please enter a filename ending with .html.
Output an obj file, please enter a filename ending with .obj.
Output a vtkjs file, please enter a filename without format.

Multi-view visualization of reconstructed 3D model. If you want to draw a legend in each sub-window, please ensure that the key names used in each legend are different.

Parameters:

model

A MultiBlock of reconstructed models or a reconstructed model.

key

The key under which are the labels.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.
Output a gif file, please enter a filename ending with .gif.
Output a mp4 file, please enter a filename ending with .mp4.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'pythreejs' - Show a pythreejs widget
'static' - Display a static figure.
'ipygany' - Show an ipygany widget
'panel' - Show a panel widget.

off_screen

Renders off-screen when True. Useful for automated screenshots.

shape

Number of sub-render windows inside the main window. By default, there is only one render window.

Specify two across with ``shape``=(2, 1) and a two by two grid with ``shape``=(2, 2).
shape Can also accept a string descriptor as shape.

E.g.: shape="3|1" means 3 plots on the left and 1 on the right, E.g.: shape="4/2" means 4 plots on top and 2 at the bottom.

window_size

Window size in pixels. The default window_size is [512, 512].

background

The background color of the window.

cpo

Camera position of the active render window. Available cpo are:

Iterable containing position, focal_point, and view up.
E.g.: [(2.0, 5.0, 13.0), (0.0, 0.0, 0.0), (-0.7, -0.5, 0.3)].
Iterable containing a view vector.
E.g.: [-1.0, 2.0, -5.0].
A string containing the plane orthogonal to the view direction.
E.g.: 'xy', 'xz', 'yz', 'yx', 'zx', 'zy', 'iso'.

colormap

Name of the Matplotlib colormap to use when mapping the scalars.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

opacity

Opacity of the model.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

model_style

Visualization style of the model. One of the following:

model_style = 'surface',
model_style = 'wireframe',
model_style = 'points'.

model_size

If model_style = 'points', point size of any nodes in the dataset plotted.

If model_style = 'wireframe', thickness of lines.

show_legend

whether to add a legend to the plotter.

legend_kwargs

show_outline

whether to produce an outline of the full extent for the model.

outline_kwargs

A dictionary that will be pass to the add_outline function.

text

The text to add the rendering.

text_kwargs

A dictionary that will be pass to the add_text function.

view_up

The normal to the orbital plane. Only available when filename ending with .mp4 or .gif.

framerate

Frames per second. Only available when filename ending with .mp4 or .gif.

plotter_filename

The filename of the file where the plotter is saved.: Writer type is inferred from the extension of the filename.

Output a gltf file, please enter a filename ending with .gltf.
Output a html file, please enter a filename ending with .html.
Output an obj file, please enter a filename ending with .obj.
Output a vtkjs file, please enter a filename without format.

spateo.plotting.static.three_d_plot.three_d_plot(model: pyvista.PolyData | pyvista.UnstructuredGrid | pyvista.MultiBlock, key: str | list = None, filename: str | None = None, jupyter: bool | Literal[panel, none, pythreejs, static, ipygany] = False, off_screen: bool = False, window_size: tuple = (512, 512), background: str = 'white', cpo: str | list = 'iso', colormap: str | list | None = None, ambient: float | list = 0.2, opacity: float | numpy.ndarray | list = 1.0, model_style: Literal[points, surface, wireframe] | list = 'surface', model_size: float | list = 3.0, show_legend: bool = True, legend_kwargs: dict | None = None, show_outline: bool = False, outline_kwargs: dict | None = None, text: str | None = None, text_kwargs: dict | None = None, view_up: tuple = (0.5, 0.5, 1), framerate: int = 24, plotter_filename: str | None = None)[source]#

Visualize reconstructed 3D model.

Parameters:

model

A reconstructed model.

key

The key under which are the labels.

filename

Filename of output file. Writer type is inferred from the extension of the filename.

Output an image file,please enter a filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.
Output a gif file, please enter a filename ending with .gif.
Output a mp4 file, please enter a filename ending with .mp4.

jupyter

Whether to plot in jupyter notebook. Available jupyter are:

'none' - Do not display in the notebook.
'pythreejs' - Show a pythreejs widget
'static' - Display a static figure.
'ipygany' - Show an ipygany widget
'panel' - Show a panel widget.

off_screen

Renders off-screen when True. Useful for automated screenshots.

window_size

Window size in pixels. The default window_size is [512, 512].

background

The background color of the window.

cpo

Camera position of the active render window. Available cpo are:

Iterable containing position, focal_point, and view up.
E.g.: [(2.0, 5.0, 13.0), (0.0, 0.0, 0.0), (-0.7, -0.5, 0.3)].
Iterable containing a view vector.
E.g.: [-1.0, 2.0, -5.0].
A string containing the plane orthogonal to the view direction.
E.g.: 'xy', 'xz', 'yz', 'yx', 'zx', 'zy', 'iso'.

colormap

Name of the Matplotlib colormap to use when mapping the scalars.

When the colormap is None, use {key}_rgba to map the scalars, otherwise use the colormap to map scalars.

ambient

When lighting is enabled, this is the amount of light in the range of 0 to 1 (default 0.0) that reaches the actor when not directed at the light source emitted from the viewer.

opacity

Opacity of the model.

A string can also be specified to map the scalars range to a predefined opacity transfer function (options include: ‘linear’, ‘linear_r’, ‘geom’, ‘geom_r’).

model_style

Visualization style of the model. One of the following:

model_style = 'surface',
model_style = 'wireframe',
model_style = 'points'.

model_size

If model_style = 'points', point size of any nodes in the dataset plotted.

If model_style = 'wireframe', thickness of lines.

show_legend

whether to add a legend to the plotter.

legend_kwargs

show_outline

whether to produce an outline of the full extent for the model.

outline_kwargs

A dictionary that will be pass to the add_outline function.

text

The text to add the rendering.

text_kwargs

A dictionary that will be pass to the add_text function.

view_up

The normal to the orbital plane. Only available when filename ending with .mp4 or .gif.

framerate

Frames per second. Only available when filename ending with .mp4 or .gif.

plotter_filename

The filename of the file where the plotter is saved.: Writer type is inferred from the extension of the filename.

Output a gltf file, please enter a filename ending with .gltf.
Output a html file, please enter a filename ending with .html.
Output an obj file, please enter a filename ending with .obj.
Output a vtkjs file, please enter a filename without format.

Returns:

List of camera position, focal point, and view up.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.
img: Numpy array of the last image.: Returned only if filename is None or filename ending with '.png', '.tif', '.tiff', '.bmp', '.jpeg', '.jpg', '.svg', '.eps', '.ps', '.pdf', '.tex'.

Return type:

cpo

spateo.plotting.static.three_d_plot#

Submodules#

Package Contents#

Functions#

`spateo.plotting.static.three_d_plot`#