spateo.tdr.models.models_individual.point_clouds
================================================

.. py:module:: spateo.tdr.models.models_individual.point_clouds


Functions
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.. autoapisummary::

   spateo.tdr.models.models_individual.point_clouds.construct_pc


Module Contents
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.. py:function:: construct_pc(adata: anndata.AnnData, layer: str = 'X', 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) -> Tuple[pyvista.PolyData, Optional[str]]

   Construct a point cloud model based on 3D coordinate information.

   :param adata: AnnData object.
   :param layer: If ``'X'``, uses ``.X``, otherwise uses the representation given by ``.layers[layer]``.
   :param spatial_key: The key in ``.obsm`` that corresponds to the spatial coordinate of each bucket.
   :param groupby: The key that stores clustering or annotation information in ``.obs``,
                   a gene name or a list of gene names in ``.var``.
   :param key_added: The key under which to add the labels.
   :param mask: The part that you don't want to be displayed.
   :param colormap: Colors to use for plotting pc. The default colormap is ``'rainbow'``.
   :param 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]``, the ``groupby`` information.
                 ``pc.point_data[f'{key_added}_rgba']``, the rgba colors of the ``groupby`` information.
                 ``pc.point_data['obs_index']``, the obs_index of each coordinate in the original adata.
             plot_cmap: Recommended colormap parameter values for plotting.
   :rtype: pc