scvelo.utils.get_cell_transitions

scvelo.utils.get_cell_transitions(adata, starting_cell=0, basis=None, n_steps=100, n_neighbors=30, backward=False, random_state=None, **kwargs)

Simulate cell transitions

Parameters:
adata : AnnData

Annotated data matrix.

starting_cell : int (default: 0)

Name of velocity estimates to be used.

basis : str or None (default: None)

Key for embedding coordinates.s

n_steps : int (default: 100)

Number of transitions/steps to be simulated.

backward : bool (default: False)

Whether to use the transition matrix to push forward (False) or to pull backward (True)

random_state : int or None (default: None)

Set to int for reproducibility, otherwise None for a random seed.

**kwargs

To be passed to tl.transition_matrix.

Returns:

  • Returns embedding coordinates (if basis is specified),
  • otherwise return indices of simulated cell transitions.