cellrank.tl.estimators.GPCCA.set_terminal_states

GPCCA.set_terminal_states(labels, cluster_key=None, add_to_existing=False, **kwargs)

Manually define terminal states.

Parameters

• labels (Union[Series, Dict[str, Sequence[Any]]]) –

  Defines the terminal states. Valid options are:

  • categorical pandas.Series where each category corresponds to a terminal state. NaN entries denote cells that do not belong to any terminal state, i.e. these are either initial or transient cells.

  • dict where keys are terminal states and values are lists of cell barcodes corresponding to annotations in adata.AnnData.obs_names. If only 1 key is provided, values should correspond to terminal state clusters if a categorical pandas.Series can be found in anndata.AnnData.obs.

• cluster_key (Optional[str]) – Key in anndata.AnnData.obs in order to associate names and colors with terminal_states. Each terminal state will be given the name and color corresponding to the cluster it mostly overlaps with.

• add_to_existing (bool) – Whether the new terminal states should be added to pre-existing ones. Cells already assigned to a terminal state will be re-assigned to the new terminal state if there’s a conflict between old and new annotations. This throws an error if no previous annotations corresponding to terminal states have been found.

Return type

None

Returns

Nothing, just updates the following fields:

• terminal_states - Categorical annotation of terminal states.

• terminal_states_probabilities - Aggregated probability of cells to be in terminal states.