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.

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 : {‘connectivity’, ‘distance’}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 : float | NoneOptional[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



igraph object