dynamo.tl.infomap
- dynamo.tl.infomap(adata, use_weight=True, adj_matrix=None, adj_matrix_key=None, result_key=None, layer=None, obsm_key=None, selected_cluster_subset=None, selected_cell_subset=None, directed=False, copy=False, **kwargs)[source]
Apply infomap community detection algorithm to cluster adata.
For other community detection general parameters, please refer to dynamo’s tl.cluster_community function. “Infomap is based on ideas of information theory. The algorithm uses the probability flow of random walks on a network as a proxy for information flows in the real system and it decomposes the network into modules by compressing a description of the probability flow.” - cdlib
- Parameters:
adata (
AnnData
) – an AnnData object.use_weight (
bool
) – whether to use graph weight or not. False means to use connectivities only (0/1 integer values). Defaults to True.adj_matrix (
Union
[ndarray
,csr_matrix
,None
]) – adj_matrix used for clustering. Defaults to None.adj_matrix_key (
Optional
[str
]) – the key for adj_matrix stored in adata.obsp. Defaults to None.result_key (
Optional
[str
]) – the key where the results will be stored in obs. Defaults to None.layer (
Optional
[str
]) – the adata layer on which cluster algorithms will work. Defaults to None.obsm_key (
Optional
[str
]) – the key in obsm corresponding to the data that would be used for finding neighbors. Defaults to None.selected_cluster_subset (
Optional
[Tuple
[str
,str
]]) – a tuple of (cluster_key, allowed_clusters).Filtering cells in adata based on cluster_key in adata.obs and only reserve cells in the allowed clusters. Defaults to None.selected_cell_subset (
Union
[List
[int
],List
[str
],None
]) – a subset of cells in adata that would be clustered. Could be a list of indices or a list of cell names. Defaults to None.directed (
bool
) – whether the edges in the graph should be directed. Defaults to False.copy (
bool
) – whether to return a new updated AnnData object or updated the original one inplace. Defaults to False.
- Return type:
- Returns:
An updated AnnData object if copy is set to be true.