def test_adaptive_kernel_constants(self, adata: AnnData):
ck1 = ConnectivityKernel(adata).compute_transition_matrix()
ck1._mat_scaler = np.random.normal(size=(adata.n_obs, adata.n_obs))
ck2 = ConnectivityKernel(adata).compute_transition_matrix()
ck2._mat_scaler = np.random.normal(size=(adata.n_obs, adata.n_obs))
k = (3 * ck1) ^ (1 * ck2)
k.compute_transition_matrix()
assert k[0][0]._value == 3 / 4
assert k[1][0]._value == 1 / 4
def create_kernels(
adata: AnnData,
velocity_variances: Optional[str] = None,
connectivity_variances: Optional[str] = None,
) -> Tuple[VelocityKernel, ConnectivityKernel]:
vk = VelocityKernel(adata)
vk._mat_scaler = adata.uns.get(
velocity_variances, np.random.normal(size=(adata.n_obs, adata.n_obs))
)
ck = ConnectivityKernel(adata)
ck._mat_scaler = adata.uns.get(
connectivity_variances, np.random.normal(size=(adata.n_obs, adata.n_obs))
)
vk._transition_matrix = csr_matrix(np.eye(adata.n_obs))
ck._transition_matrix = np.eye(adata.n_obs, k=1) / 2 + np.eye(adata.n_obs) / 2
ck._transition_matrix[-1, -1] = 1
ck._transition_matrix = csr_matrix(ck._transition_matrix)
np.testing.assert_allclose(
np.sum(ck._transition_matrix.A, axis=1), 1
) # sanity check
return vk, ck
def test_adaptive_kernel_complex(self, adata: AnnData):
ck1 = ConnectivityKernel(adata).compute_transition_matrix()
ck1._mat_scaler = np.random.normal(size=(adata.n_obs, adata.n_obs))
ck2 = ConnectivityKernel(adata).compute_transition_matrix()
ck2._mat_scaler = np.random.normal(size=(adata.n_obs, adata.n_obs))
ck3 = ConnectivityKernel(adata).compute_transition_matrix()
ck3._mat_scaler = np.random.normal(size=(adata.n_obs, adata.n_obs))
k = 4 * ((3 * ck1) ^ (1 * ck2)) + 2 * ck3
k.compute_transition_matrix()
assert k[0][0].transition_matrix == 4 / 6
assert k[1][0].transition_matrix == 2 / 6
assert k[0][1][0][0]._value == 3 / 4
assert k[0][1][1][0]._value == 1 / 4
