b3505e7e9e08a389dfff5788db2b6634abdeb1cd,scanpy/tools/_dpt.py,,_diffmap,#Any#Any#,14

Before Change

    dpt.compute_eigen(n_comps=n_comps)
    adata.obsm["X_diffmap"] = dpt.eigen_basis
    adata.uns["diffmap_evals"] = dpt.eigen_values
    logg.info("    finished", time=True, end=" " if _settings_verbosity_greater_or_equal_than(3) else "\n")
    logg.hint("added\n"
              "    \"X_diffmap\", diffmap coordinates (adata.obsm)\n"
              "    \"diffmap_evals\", eigenvalues of transition matrix (adata.uns)")

After Change

def _diffmap(adata, n_comps=15):
    start = logg.info(f"computing Diffusion Maps using n_comps={n_comps}(=n_dcs)")
    dpt = DPT(adata)
    dpt.compute_transitions()
    dpt.compute_eigen(n_comps=n_comps)
    adata.obsm["X_diffmap"] = dpt.eigen_basis

Instances