plastro.overlap.PLASTRO_overlaps

plastro.overlap.PLASTRO_overlaps(character_matrix: DataFrame, ad: AnnData, maximum_radius: int = 500, interval: int = 1, latent_space_key: str = 'X_dm', parallel: bool = False, save_to: str | None = None) → DataFrame[source]

Compute overlaps between lineage and phenotypic neighborhoods.

For each cell and radius, computes the overlap between cells that are lineage neighbors (similar character states) and phenotypic neighbors (close in latent space).

Parameters:

  • character_matrix (pd.DataFrame) – Character matrix with mutation data.

  • ad (anndata.AnnData) – Annotated data object with phenotypic information.

  • maximum_radius (int, optional) – Maximum neighborhood radius, by default 500.

  • interval (int, optional) – Radius increment, by default 1.

  • latent_space_key (str, optional) – Key for latent space coordinates, by default ‘X_dm’.

  • parallel (bool, optional) – Use parallel processing, by default False.

  • save_to (str, optional) – Save directory, by default None.

Returns:

Overlap values for each cell (rows) at each radius (columns).

Return type:

pd.DataFrame