nichepca.graph_construction.remove_long_links

nichepca.graph_construction.remove_long_links(adata=None, edge_index=None, edge_weight=None, dist_percentile=99.0, copy=False)

Remove links with a distance larger than a given percentile.

Parameters:

• adata (AnnData | None (default: None)) – Annotated data object.

• edge_index (ndarray | None (default: None)) – Edge index of the graph.

• edge_weight (ndarray | None (default: None)) – Edge weight of the graph.

• dist_percentile (float (default: 99.0)) – Percentile threshold for the maximum edge weight.

• copy (bool (default: False)) – Whether to return a copy of the graph.

Returns:

Tuple[np.ndarray, np.ndarray] | None If copy=True, returns the edge index and edge weight. Otherwise, stores the new edge index and edge weight in adata.uns.

Notes

This function is inspired by the remove_long_links function in the cellcharter package CSOgroup/cellcharter.