tirank.SCSTpreprocess.compute_similarity

tirank.SCSTpreprocess.compute_similarity(savePath, ann_data, calculate_distance=False)[source]

Extracts and saves the cell/spot similarity matrix (connectivities).

Optionally, it can also calculate a spatial distance-based adjacency matrix (6 nearest neighbors) for ST data.

Parameters:

  • savePath (str) – The main project directory path.

  • ann_data (sc.AnnData) – A clustered AnnData object (must have ann_data.obsp[‘connectivities’]).

  • calculate_distance (bool, optional) – Whether to compute the spatial distance matrix (ST only). Defaults to False.

Returns:

None