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]))