scvelo.tl.velocity_pseudotime

scvelo.tl.velocity_pseudotime(adata, vkey='velocity', groupby=None, groups=None, root=None, end=None, n_dcs=10, use_velocity_graph=True, save_diffmap=None, return_model=None, **kwargs)

Computes a pseudotime based on the velocity graph.

Velocity pseudotime is a random-walk based distance measures on the velocity graph. After computing a distribution over root cells obtained from the velocity-inferred transition matrix, it measures the average number of steps it takes to reach a cell after start walking from one of the root cells. Contrarily to diffusion pseudotime, it implicitly infers the root cells and is based on the directed velocity graph instead of the similarity-based diffusion kernel.

scv.tl.velocity_pseudotime(adata)
scv.pl.scatter(adata, color='velocity_pseudotime', color_map='gnuplot')
https://user-images.githubusercontent.com/31883718/69545487-33fbc000-0f92-11ea-969b-194dc68400b0.png
Parameters:
adata : AnnData

Annotated data matrix

vkey : str (default: ‘velocity’)

Name of velocity estimates to be used.

groupby : str, list or np.ndarray (default: None)

Key of observations grouping to consider.

groups : str, list or np.ndarray (default: None)

Groups selected to find terminal states on. Must be an element of adata.obs[groupby].

root : int (default: None)

Index of root cell to be used. Computed from velocity-inferred transition matrix if not specified.

end : int (default: None)

Index of end point to be used. Computed from velocity-inferred transition matrix if not specified.

n_dcs : int (default: 10)

The number of diffusion components to use.

use_velocity_graph : bool (default: True)

Whether to use the velocity graph. If False, it uses the similarity-based diffusion kernel.

save_diffmap : bool (default: None)

Whether to store diffmap coordinates.

return_model : bool (default: None)

Whether to return the vpt object for further inspection.

**kwargs

Further arguments to pass to VPT, such as min_group_size, allow_kendall_tau_shift, and n_branchings.

Returns

-------

adata with the attributes : Updates

velocity_pseudotime : .obs

Velocity pseudotime obtained from velocity graph.