spateo.tdr.models.models_individual.point_clouds
#
Module Contents#
Functions#
|
Construct a point cloud model based on 3D coordinate information. |
- spateo.tdr.models.models_individual.point_clouds.construct_pc(adata: anndata.AnnData, layer: str = 'X', spatial_key: str = 'spatial', groupby: str | tuple = None, key_added: str = 'groups', mask: str | int | float | list = None, colormap: str | list | dict = 'rainbow', alphamap: float | list | dict = 1.0) Tuple[pyvista.PolyData, str | None] [source]#
Construct a point cloud model based on 3D coordinate information.
- Parameters:
- adata
AnnData object.
- layer
If
'X'
, uses.X
, otherwise uses the representation given by.layers[layer]
.- spatial_key
The key in
.obsm
that corresponds to the spatial coordinate of each bucket.- groupby
The key that stores clustering or annotation information in
.obs
, a gene name or a list of gene names in.var
.- key_added
The key under which to add the labels.
- mask
The part that you don’t want to be displayed.
- colormap
Colors to use for plotting pc. The default colormap is
'rainbow'
.- alphamap
The opacity of the colors to use for plotting pc. The default alphamap is
1.0
.
- Returns:
- A point cloud, which contains the following properties:
pc.point_data[key_added]
, thegroupby
information.pc.point_data[f'{key_added}_rgba']
, the rgba colors of thegroupby
information.pc.point_data['obs_index']
, the obs_index of each coordinate in the original adata.
plot_cmap: Recommended colormap parameter values for plotting.
- Return type:
pc