def test_interaction_matrix_values(adata_intmat: AnnData):
result_weighted = interaction_matrix(adata_intmat,
"cat",
weights=True,
copy=True)
result_unweighted = interaction_matrix(adata_intmat,
"cat",
weights=False,
copy=True)
expected_weighted = np.array([
[5, 1],
[2, 3],
])
expected_unweighted = np.array([
[4, 1],
[2, 2],
])
np.testing.assert_array_equal(expected_weighted, result_weighted)
np.testing.assert_array_equal(expected_unweighted, result_unweighted)
def test_interaction_matrix_nan_values(adata_intmat: AnnData):
adata_intmat.obs["cat"].iloc[0] = np.nan
result_weighted = interaction_matrix(adata_intmat,
"cat",
weights=True,
copy=True)
result_unweighted = interaction_matrix(adata_intmat,
"cat",
weights=False,
copy=True)
expected_weighted = np.array([
[2, 1],
[2, 3],
])
expected_unweighted = np.array([
[1, 1],
[2, 2],
])
np.testing.assert_array_equal(expected_weighted, result_weighted)
np.testing.assert_array_equal(expected_unweighted, result_unweighted)
def test_interaction_matrix_normalize(nhood_data: AnnData, normalized: bool):
adata = nhood_data
res = interaction_matrix(
adata=adata,
cluster_key=_CK,
connectivity_key="spatial",
copy=True,
normalized=normalized,
)
n_cls = adata.obs["leiden"].nunique()
assert isinstance(res, np.ndarray)
assert res.shape == (n_cls, n_cls)
if normalized:
np.testing.assert_allclose(res.sum(1), 1.0), res.sum(1)
else:
assert len(adata.obsp["spatial_connectivities"].data) == res.sum()
def test_interaction_matrix_copy(nhood_data: AnnData, copy: bool):
adata = nhood_data
res = interaction_matrix(
adata=adata,
cluster_key=_CK,
connectivity_key="spatial",
copy=copy,
)
key = Key.uns.interaction_matrix(_CK)
n_cls = adata.obs[_CK].nunique()
if not copy:
assert res is None
assert key in adata.uns_keys()
res = adata.uns[key]
else:
assert key not in adata.uns_keys()
assert isinstance(res, np.ndarray)
assert res.shape == (n_cls, n_cls)
def test_plot_interaction_dendro(self, adata: AnnData):
gr.spatial_neighbors(adata)
gr.interaction_matrix(adata, cluster_key=C_KEY)
pl.interaction_matrix(adata, cluster_key=C_KEY, method="single")
def test_plot_interaction(self, adata: AnnData):
gr.spatial_neighbors(adata)
gr.interaction_matrix(adata, cluster_key=C_KEY)
pl.interaction_matrix(adata, cluster_key=C_KEY)