scvelo.tl.louvain¶

scvelo.tl.
louvain
(adata, resolution=None, random_state=0, restrict_to=None, key_added='louvain', adjacency=None, flavor='vtraag', directed=True, use_weights=False, partition_type=None, partition_kwargs=mappingproxy({}), neighbors_key=None, obsp=None, copy=False)¶ Cluster cells into subgroups [Blondel08] [Levine15] [Traag17].
Cluster cells using the Louvain algorithm [Blondel08] in the implementation of [Traag17]. The Louvain algorithm has been proposed for singlecell analysis by [Levine15].
This requires having ran
neighbors()
orbbknn()
first, or explicitly passing aadjacency
matrix.Parameters:  adata :
AnnData
The annotated data matrix.
 resolution :
float
,None
For the default flavor (
'vtraag'
), you can provide a resolution (higher resolution means finding more and smaller clusters), which defaults to 1.0. See “Time as a resolution parameter” in [Lambiotte09]. random_state :
None
,int
,RandomState
Change the initialization of the optimization.
 restrict_to :
Tuple
[str
,Sequence
[str
]],None
Restrict the clustering to the categories within the key for sample annotation, tuple needs to contain
(obs_key, list_of_categories)
. key_added :
str
Key under which to add the cluster labels. (default:
'louvain'
) adjacency :
spmatrix
,None
Sparse adjacency matrix of the graph, defaults to neighbors connectivities.
 flavor :
_Genericalias
[vtraag, igraph, rapids] Choose between to packages for computing the clustering.
'vtraag'
is much more powerful, and the default. directed :
bool
Interpret the
adjacency
matrix as directed graph? use_weights :
bool
Use weights from knn graph.
 partition_type :
Type
[MutableVertexPartition
],None
Type of partition to use. Only a valid argument if
flavor
is'vtraag'
. partition_kwargs :
Mapping
[str
,Any
] Key word arguments to pass to partitioning, if
vtraag
method is being used. neighbors_key :
str
,None
Use neighbors connectivities as adjacency. If not specified, louvain looks .obsp[‘connectivities’] for connectivities (default storage place for pp.neighbors). If specified, louvain looks .obsp[.uns[neighbors_key][‘connectivities_key’]] for connectivities.
 obsp :
str
,None
Use .obsp[obsp] as adjacency. You can’t specify both obsp and neighbors_key at the same time.
 copy :
bool
Copy adata or modify it inplace.
Return type: AnnData
,None
Returns:  adata :