pegasus.calc_pseudotime¶
- pegasus.calc_pseudotime(data, roots)[source]¶
Calculate Pseudotime based on Diffusion Map.
- Parameters
data (
anndata.AnnData
) – Annotated data matrix with rows for cells and columns for genes.roots (
List[str]
) – List of cell barcodes in the data.
- Return type
None
- Returns
None
Update
data.obs
–data.obs["pseudotime"]
: Pseudotime result.
Examples
>>> pg.calc_pseudotime(adata, roots = list(adata.obs_names[0:100]))