lynx.trajectory.compute_pseudotime

lynx.trajectory.compute_pseudotime(adata, principal_graph, n_nodes=20, use_rep='X_z', source=None, seed=42, root_marker=None)[source]

Compute pseudotime (t) in [0, 1] along the given principal graph fitted onto the latent space (adata.obsm[use_rep]); Use optional marker to rotate the (+/-) sign of the trajectory at which the root_marker enriches

Parameters:

  • adata (sc.AnnData) – AnnData of latent representation w/ computed elastic principal graph

  • root_marker (str) – Optional marker close to ‘root’ to rotate (+/-) of the trajectory

  • use_rep (str) – Use the indicated representation. ‘X’ or any key for .obsm is valid. If None, the representation is chosen automatically

  • n_nodes (int) – # principal nodes to infer Increase n_nodes get more localized principal manifold

  • principal_graph (dict)

  • source (int | None)

  • seed (int)