def test_sample_idx_wrong_length():
with assert_raises_message(
ValueError,
"sample_idx (10) must be the same length as data ({})".format(
data.shape[0]),
):
build_graph(data, graphtype="mnn", sample_idx=np.arange(10))
def test_sample_idx_and_precomputed():
build_graph(
squareform(pdist(data)),
n_pca=None,
sample_idx=np.arange(10),
precomputed="distance",
decay=10,
)
def test_sample_idx_and_precomputed():
with assert_raises_message(
ValueError,
"MNNGraph does not support precomputed values. Use `graphtype='exact'` and `sample_idx=None` or `precomputed=None`",
):
build_graph(data,
n_pca=None,
sample_idx=np.arange(10),
precomputed="distance")
def test_build_exact_with_sample_idx():
with assert_raises_message(
ValueError,
"TraditionalGraph does not support batch correction. Use `graphtype='mnn'` or `sample_idx=None`",
):
build_graph(data,
graphtype="exact",
sample_idx=np.arange(len(data)),
decay=10)
def test_sample_idx_wrong_length():
build_graph(data, graphtype="mnn", sample_idx=np.arange(10))
def test_sample_idx_and_precomputed():
build_graph(data, n_pca=None, sample_idx=np.arange(10), precomputed="distance")
def test_build_knn_with_sample_idx():
with assert_raises_message(
ValueError,
"kNNGraph does not support batch correction. Use `graphtype='mnn'` or `sample_idx=None`",
):
build_graph(data, graphtype="knn", sample_idx=np.arange(len(data)))
def test_build_knn_with_sample_idx():
build_graph(data, graphtype='knn', sample_idx=np.arange(len(data)))
def test_build_exact_with_sample_idx():
build_graph(data,
graphtype='exact',
sample_idx=np.arange(len(data)),
decay=10)