cospar.pl.single_cell_transition

cospar.pl.single_cell_transition(adata, selected_state_id_list, source='transition_map', map_backward=True, savefig=False, initial_point_size=3, color_bar=True)

Plot transition probability from given initial cell states.

If map_backward=True, plot the probability \(T_{ij}\) over initial states \(i\) at a given later state \(j\). Otherwise, plot the probability \(T_{ij}\) over later states \(j\) at a fixed initial state \(i\).

Parameters

adata : AnnData object

Assume to contain transition maps at adata.uns.

selected_state_id_list : list

List of cell id’s. Like [0,1,2].

source : str

The transition map to be used for plotting: {‘transition_map’, ‘intraclone_transition_map’,…}. The actual available map depends on adata itself, which can be accessed at adata.uns[‘available_map’]

map_backward : bool, optional (default: True)

If map_backward=True, plot the probability of source states where the current cell state comes from; otherwise, plot future state probability starting from given initial state.

initial_point_size : int, optional (default: 3)

Relative size of the data point for the selected cells.

save_fig : bool, optional (default: False)

If true, save figure to defined directory at settings.figure_path

color_bar : bool, optional (default: True)

Plot the color bar.