spateo.tdr.models.pc.pc_model
#
Module Contents#
Functions#
|
Construct a point cloud model based on 3D coordinate information. |
- spateo.tdr.models.pc.pc_model.construct_pc(adata: anndata.AnnData, spatial_key: str = 'spatial', groupby: Union[str, tuple] = None, key_added: str = 'groups', mask: Union[str, int, float, list] = None, colormap: Union[str, list, dict] = 'rainbow', alphamap: Union[float, list, dict] = 1.0) pyvista.PolyData [source]#
Construct a point cloud model based on 3D coordinate information.
- Parameters
- adata
AnnData object.
- 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 pcd. The default colormap is
'rainbow'
.- alphamap
The opacity of the colors to use for plotting pcd. 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.
- Return type
pc