cellcharter.gr.remove_long_links

cellcharter.gr.remove_long_links(adata, distance_percentile=99.0, connectivity_key=None, distances_key=None, neighs_key=None, copy=False)

Remove links between cells at a distance bigger than a certain percentile of all positive distances.

It is designed for data with generic coordinates.

Parameters:

• adata (AnnData) – Annotated data object.

• distance_percentile (float (default: 99.0)) – Percentile of the distances between cells over which links are trimmed after the network is built.

• connectivity_key (Optional[str] (default: None)) – Key in anndata.AnnData.obsp where spatial connectivities are stored. Default is: anndata.AnnData.obsp ['spatial_connectivities'].

• distances_key (Optional[str] (default: None)) – Key in anndata.AnnData.obsp where spatial distances are stored. Default is: anndata.AnnData.obsp ['{{Key.obsp.spatial_dist()}}'].

• neighs_key (Optional[str] (default: None)) – Key in anndata.AnnData.uns where the parameters from gr.spatial_neighbors are stored. Default is: anndata.AnnData.uns ['{{Key.uns.spatial_neighs()}}'].

• copy (bool (default: False)) – If True, return the result, otherwise save it to the adata object.

Return type:

tuple[csr_matrix, csr_matrix] | None

Returns:

If copy = True, returns a tuple with the new spatial connectivities and distances matrices.

Otherwise, modifies the adata with the following keys:

• anndata.AnnData.obsp ['{{connectivity_key}}'] - the new spatial connectivities.

• anndata.AnnData.obsp ['{{distances_key}}'] - the new spatial distances.

• anndata.AnnData.uns ['{{neighs_key}}'] - dict containing parameters.