cospar.pl.fate_map¶

cospar.pl.fate_map(adata, selected_fates=None, source='transition_map', selected_times=None, background=True, show_histogram=False, plot_target_state=False, auto_color_scale=True, color_bar=True, target_transparency=0.2, figure_index='', mask=None, color_map=<matplotlib.colors.LinearSegmentedColormap object>, **kwargs)¶

Plot transition probability to given fate/ancestor clusters.

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

Parameters

adata : AnnData object: Assume to contain transition maps at adata.uns.
selected_fates : list: List of cluster ids consistent with adata.obs[‘state_info’]. It allows a nested structure. If so, we merge clusters within each sub-list into a mega-fate cluster.
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’]
selected_times : list, optional (default: all): A list of time points to further restrict the cell states to plot. The default choice is not to constrain the cell states to show.
background : bool, optional (default: True): If true, plot all cell states (t1+t2) in grey as the background.
show_histogram : bool, optional (default: False): If true, show the distribution of inferred fate probability.
plot_target_state: If True, plot target states.
color_bar : bool, optional (default: True): plot the color bar if True.
auto_color_scale: True: automatically rescale the color range to match the value range.
target_transparency : float, optional (default: 0.2): It controls the transparency of the plotted target cell states, for visual effect. Range: [0,1].
figure_index : str, optional (default: ‘’): String index for annotate filename for saved figures. Used to distinuigh plots from different conditions.
mask : np.array, optional (default: None): A boolean array for available cell states. It should has the length as adata.shape[0]. Especially useful to constrain the states to show fate bias.
color_map: The color map (a matplotlib.pyplot.cm object) to visualize the result.