scvelo.tl.rank_velocity_genes

scvelo.tl.rank_velocity_genes(data, vkey='velocity', n_genes=10, groupby=None, match_with=None, resolution=None, min_counts=None, min_r2=None, min_dispersion=None, min_likelihood=None, copy=False)

Rank genes for velocity characterizing groups.

Parameters:
data : AnnData

Annotated data matrix.

vkey : str (default: ‘velocity’)

Key of velocities computed in tl.velocity

n_genes : int, optional (default: 100)

The number of genes that appear in the returned tables.

groupby : str, list or np.ndarray (default: None)

Key of observations grouping to consider.

match_with : str or None (default: None)

adata.obs key to separatively rank velocities on.

resolution : str or None (default: None)

Resolution for louvain modularity.

min_counts : float (default: None)

Minimum count of genes for consideration.

min_r2 : float (default: None)

Minimum r2 value of genes for consideration.

min_dispersion : float (default: None)

Minimum dispersion norm value of genes for consideration.

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
  • rank_velocity_genes (.uns) – Structured array to be indexed by group id storing the gene names. Ordered according to scores.
  • velocity_score (.var) – Storing the score for each gene for each group. Ordered according to scores.