scirpy.util.graph.igraph_from_sparse_matrix

scirpy.util.graph.igraph_from_sparse_matrix(matrix, *, matrix_type='distance', max_value=None, simplify=True)

Get an igraph object from an adjacency or distance matrix.

Parameters:

• matrix (spmatrix) – A sparse matrix that represents the connectivity or distance matrix for the graph. Zero-entries mean “no edge between the two nodes”.

• matrix_type (Literal['connectivity', 'distance'] (default: 'distance')) – Whether the sparse_matrix represents connectivities (higher value = smaller distance) or distances (higher value = higher distance). Distance matrices will be converted into connectivities. A connectivity matrix is also known as weighted adjacency matrix.

• max_value (Optional[float] (default: None)) – When converting distances to connectivities, this will be considered the maximum distance. This defaults to numpy.max(sparse_matrix).

• simplify (bool (default: True)) – Make an undirected graph and remove circular edges (i.e. edges from a node to itself).

Return type:

Graph

Returns:

igraph object