spateo.plotting.static.three_d_plot.align_plots
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Module Contents#
Functions#
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Visualize multiple models separately in one figure. |
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- spateo.plotting.static.three_d_plot.align_plots._check_cpos_in_multi_plot(models: List, window_size: tuple | None = None, cpo: str | list = 'xy')[source]#
- spateo.plotting.static.three_d_plot.align_plots.multi_models(*adata: anndata.AnnData, layer: str = 'X', group_key: str | list = None, spatial_key: str = 'align_spatial', id_key: str = 'slices', mode: Literal[single, overlap, both] = 'single', center_zero: bool = False, 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 = None, background: str = 'white', colormap: str | list | dict = 'red', overlap_cmap: str | list | dict = 'dodgerblue', alphamap: float | list | dict = 1.0, overlap_amap: float | list | dict = 0.5, ambient: float | list = 0.2, opacity: float | numpy.ndarray | list = 1.0, model_size: float | list = 3.0, 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 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'
. Whenjupyter=False
, if you want to save ‘.png’ file, please ensureoff_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.
- 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.
- spateo.plotting.static.three_d_plot.align_plots.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]#