2e118aa72650e23463cf0f845198189ed9a83472,scanpy/tools/dpt.py,,dpt,#Any#Any#Any#Any#Any#Any#,11

Before Change

    of a root cell. Either add
        adata.uns["iroot"] = root_cell_index
        adata.var["xroot"] = adata[root_cell_name, :].X"""
        logg.hint(msg)
    logg.info("performing Diffusion Pseudotime analysis", r=True)
    dpt = DPT(adata, min_group_size=min_group_size,
              n_branchings=n_branchings,
              allow_kendall_tau_shift=allow_kendall_tau_shift)

After Change

    if "neighbors" not in adata.uns:
        raise ValueError(
            "You need to run `pp.neighbors` and `tl.diffmap` first.")
    if "X_diffmap" not in adata.obsm.keys():
        raise ValueError(
            "You need to run `pp.diffmap` first.")
    if "iroot" not in adata.uns and "xroot" not in adata.var:
        logg.warn(
            "No root cell found. To compute pseudotime, pass the index or "
            "expression vector of a root cell, one of:\n"

Instances