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
Optional[int] (default:None) A numpy random seed for reproducibility for muliple mappings
- copy
bool(default:False) Return a copy instead of writing to adata.
- adata
- Returns:
adata : anndata.AnnData 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.