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.

adata: AnnData

Annotated data matrix.

starting_cell: int (default: 0)

Index (int) or name (obs_names) of starting cell.

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.


To be passed to tl.transition_matrix.


  • Returns embedding coordinates (if basis is specified),

  • otherwise return indices of simulated cell transitions.