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)) – 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.

• **kwargs – To be passed to tl.transition_matrix.

Returns:

• Returns embedding coordinates (if basis is specified),

• otherwise return indices of simulated cell transitions.