cellrank.pl.terminal_states

cellrank.pl.terminal_states(adata, discrete=False, states=None, color=None, mode='embedding', time_key='latent_time', **kwargs)[source]

Plot terminal states uncovered by cellrank.tl.terminal.

Parameters

  • adata (anndata.AnnData) – Annotated data object.

  • discrete (bool) – If True, plot probability distribution of terminal states. Only available when terminal were estimated by cellrank.tl.estimators.GPCCA.

  • states (Union[str, Sequence[str], None]) – Subset of terminal states to plot. If None, plot all terminal states.

  • color (Optional[str]) – If given, plot cluster annotations left of the terminal states.

  • mode (Literal[‘embedding’, ‘time’]) –

    Valid options are:

    • ’embedding’ - plot the embedding while coloring in continuous or categorical observations.

    • ’time’ - plot the pseudotime on x-axis and the probabilities/memberships on y-axis.

  • time_key (str) – Key in anndata.AnnData.obs where the pseudotime is stored.

  • basis – Basis to use when mode = 'embedding'. If None, use ‘umap’.

  • kwargs – Keyword arguments for cellrank.tl.estimators.GPCCA.plot_terminal_states().

Return type

Optional[AnnData]

Returns

Nothing, just plots the figure. Optionally saves it based on save.

Examples

Plot terminal states

Plot terminal states