scFates.tl.pseudotime

scFates.tl.pseudotime(adata, n_jobs=1, n_map=1, seed=None, copy=False)

Compute pseudotime.

Projects cells onto the tree, and uses distance from the root as a pseudotime value.

Parameters

adata : AnnData

Annotated data matrix.

n_jobs : int (default: 1)

Number of cpu processes to use in case of performing multiple mapping.

n_map : int (default: 1)

number of probabilistic mapping of cells onto the tree to use. If n_map=1 then likelihood cell mapping is used.

seed : int | NoneOptional[int] (default: None)

A numpy random seed for reproducibility for muliple mappings

copy : bool (default: False)

Return a copy instead of writing to adata.

Returns

adata – if copy=True it returns or else add fields to adata:

.obs[‘edge’]

assigned edge.

.obs[‘t’]

assigned pseudotime value.

.obs[‘seg’]

assigned segment of the tree.

.obs[‘milestone’]

assigned region surrounding forks and tips.

.uns[‘pseudotime_list’]

list of cell projection from all mappings.

Return type

anndata.AnnData