scvelo.tl.velocity_clusters

scvelo.tl.velocity_clusters(data, vkey='velocity', match_with='clusters', sort_by='dpt_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')
https://user-images.githubusercontent.com/31883718/69625627-484dc480-1047-11ea-847f-6607a3430427.png
Parameters:
data : AnnData

Annotated data matrix.

vkey : str (default: ‘velocity’)

Key of velocities computed in tl.velocity

match_with : str (default: ‘clusters’)

The number of genes that appear in the returned tables.

match_with

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 : str or None (default: None)

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:

  • Returns or updates data with the attributes
  • velocity_clusters (.obs) – Velocity clusters obtained from applying louvain modularity on velocity expression.