scvelo.tl.velocity_clusters¶
-
scvelo.tl.
velocity_clusters
(data, vkey='velocity', match_with='clusters', sort_by='velocity_pseudotime', resolution=None, min_likelihood=None, copy=False)¶ Computes velocity clusters via louvain on velocities.
scv.tl.velocity_clusters(adata) scv.pl.scatter(adata, color="velocity_clusters")
- data
AnnData
Annotated data matrix.
- vkey: str (default: ‘velocity’)
Key of velocities computed in tl.velocity
- match_withint, optional (default: 100)
The number of genes that appear in the returned tables.
- match_with: str (default: ‘clusters’)
Match the names of the velocity clusters with the names of this key (.obs).
- sort_by: str or None (default: ‘dpt_pseudotime’)
Sort velocity clusters by this key (.obs).
- resolution: float (default: 0.7)
Resolution for louvain modularity.
- min_likelihood: float between 0 and 1 or None (default: None)
Only rank velocity of genes with a likelihood higher than min_likelihood.
- copy: bool (default: False)
Return a copy instead of writing to data.
- Returns
velocity_clusters (.obs) – Clusters obtained from applying louvain modularity on velocity expression.
- data