save_and_compare_images('master_heatmap_std_scale_var')
sc.pl.heatmap(
adata,
adata.var_names,
'cell_type',
use_raw=False,
dendrogram=True,
show=False,
standard_scale='obs',
)
save_and_compare_images('master_heatmap_std_scale_obs')
@pytest.mark.skipif(
pkg_version("matplotlib") < version.parse('3.1'),
reason="https://github.com/mwaskom/seaborn/issues/1953",
)
@pytest.mark.parametrize(
"obs_keys,name",
[(None, "master_clustermap"),
("cell_type", "master_clustermap_withcolor")],
)
def test_clustermap(image_comparer, obs_keys, name):
save_and_compare_images = image_comparer(ROOT, FIGS, tol=15)
adata = sc.datasets.krumsiek11()
sc.pl.clustermap(adata, obs_keys)
save_and_compare_images(name)
def test_dotplot(image_comparer):
ing.neighbors(k=10)
indices = ing._indices
tree = KDTree(adata_ref.obsm['X_pca'])
true_indices = tree.query(ing._obsm['rep'], 10, return_distance=False)
num_correct = 0.0
for i in range(adata_new.n_obs):
num_correct += np.sum(np.in1d(true_indices[i], indices[i]))
percent_correct = num_correct / (adata_new.n_obs * 10)
assert percent_correct > 0.99
@pytest.mark.skipif(
pkg_version("anndata") < sc.tl._ingest.ANNDATA_MIN_VERSION,
reason=
"`AnnData.concatenate` does not concatenate `.obsm` in old anndata versions",
)
def test_ingest_function(adatas):
adata_ref = adatas[0].copy()
adata_new = adatas[1].copy()
sc.tl.ingest(
adata_new,
adata_ref,
obs='bulk_labels',
embedding_method=['umap', 'pca'],
inplace=True,
)