def test_palantir(self, adata: AnnData):
conn = _get_neighs(adata, "connectivities")
n_neighbors = _get_neighs_params(adata)["n_neighbors"]
pseudotime = adata.obs["latent_time"]
conn_biased = bias_knn(conn, pseudotime, n_neighbors)
T_1 = _normalize(conn_biased)
pk = PalantirKernel(adata,
time_key="latent_time").compute_transition_matrix(
density_normalize=False)
T_2 = pk.transition_matrix
np.testing.assert_allclose(T_1.A, T_2.A, rtol=_rtol)
def test_palantir_differ_dense_norm(self, adata):
conn = get_neighs(adata, "connectivities")
n_neighbors = get_neighs_params(adata)["n_neighbors"]
pseudotime = adata.obs["latent_time"]
conn_biased = bias_knn(conn, pseudotime, n_neighbors)
T_1 = density_normalization(conn_biased, conn)
T_1 = _normalize(T_1)
pk = PalantirKernel(adata, time_key="latent_time").compute_transition_matrix(
density_normalize=False
)
T_2 = pk.transition_matrix
assert not np.allclose(T_1.A, T_2.A, rtol=_rtol)