GPCCA.plot_absorption_probabilities(data, prop, discrete=False, lineages=None, cluster_key=None, mode='embedding', time_key='latent_time', show_dp=True, title=None, same_plot=False, cmap='viridis', **kwargs)

Plot discrete states or probabilities in an embedding.

  • discrete (bool) – Whether to plot in discrete or continuous mode.

  • lineages (Union[str, Sequence[str], None]) – Plot only these lineages. If None, plot all lineages.

  • cluster_key (Optional[str]) – Key from adata .obs for plotting categorical observations.

  • mode (str) –

    Can be either ‘embedding’ or ‘time’:

    • ’embedding’ - plot the embedding while coloring in the absorption probabilities.

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

  • time_key (str) – Key from adata .obs to use as a pseudotime ordering of the cells.

  • title (Optional[str]) – Either None, in which case titles are '{to, from} {terminal, initial} {state}', or an array of titles, one per lineage.

  • same_plot (bool) – Whether to plot the lineages on the same plot using color gradients when mode='embedding'.

  • cmap (Union[str, ListedColormap]) – Colormap to use.

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


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

Return type