capital.tl.dpt¶

capital.tl.dpt(aligned_data, alignment=None, no_prune=False)¶

Calculate pseudotime for the alignments.

If there are many alignments, you are recommended to specify which alignment is used to calculate pseudotime to save time. Use cdata.alignmentlist and capital.pl.tree_alignment to take a look at alignment data.

Parameters:

aligned_data (CapitalData) – The data matrices containing the results of CAPTIAL.
alignment (Union[str, list, None]) – Specify which alignment is used to calculate pseudotime. If None, it calculates pseudotime for all alignments, by default None.
no_prune (bool) – Specify global alignment or local alignment. If True, it calculates pseudotime using all the cells in the clusters in the alignment. If False, it uses all the cells except ones that have no corresponding cluster in the root or the leaf of the alignment, by default False.