scvelo.tl.velocity_graph¶

scvelo.tl.
velocity_graph
(data, vkey='velocity', xkey='Ms', tkey=None, basis=None, n_neighbors=None, n_recurse_neighbors=None, random_neighbors_at_max=None, sqrt_transform=False, approx=False, copy=False)¶ Computes velocity graph based on cosine similarities.
The cosine similarities are computed between velocities and potential cell state transitions.
Parameters:  data :
AnnData
Annotated data matrix.
 vkey : str (default: ‘velocity’)
Name of velocity estimates to be used.
 n_neighbors : int or None (default: None)
Use fixed number of neighbors or do recursive neighbor search (if None).
 n_recurse_neighbors : int (default: 2)
Number of recursions to be done for neighbors search.
 random_neighbors_at_max : int or None (default: None)
If number of iterative neighbors for an individual cell is higher than this threshold, a random selection of such are chosen as reference neighbors.
 sqrt_transform : bool (default: False)
Whether to variancetransform the cell states changes and velocities before computing cosine similarities.
 copy : bool (default: False)
Return a copy instead of writing to adata.
Returns:  Returns or updates adata with the attributes
 velocity_graph (.uns) – sparse matrix with transition probabilities
 data :