cospar.pl.fate_hierarchy

cospar.pl.fate_hierarchy(adata, source='transition_map', rename_fates=None, plot_history=False)

Plot fate hierarchy determined by the transition map.

The results should be pre-computed from cospar.tl.fate_hierarchy().

Parameters

adata : AnnData object

Assume to contain transition maps at adata.uns.

source : str

Choices: {‘X_clone’, ‘transition_map’, ‘intraclone_transition_map’,…}. If set to be ‘clone’, use only the clonal information. If set to be any of the precomputed transition map, use the transition map to compute the fate coupling. The actual available map depends on adata itself, which can be accessed at adata.uns[‘available_map’]

rename_fates : list, optional (default: None)

Provide new names in substitution of names in selected_fates. For this to be effective, the new name list needs to have names in exact correspondence to those in the old list.

plot_history

True: plot the history of iterations.

Returns

ax – The axis object of this plot.