def test_linear_scvi(save_path):
adata = synthetic_iid()
adata = adata[:, :10].copy()
setup_anndata(adata)
model = LinearSCVI(adata, n_latent=10)
model.train(1, check_val_every_n_epoch=1, train_size=0.5)
assert len(model.history["elbo_train"]) == 1
assert len(model.history["elbo_validation"]) == 1
model.get_loadings()
model.differential_expression(groupby="labels", group1="label_1")
model.differential_expression(groupby="labels", group1="label_1", group2="label_2")
def test_linear_scvi():
adata = synthetic_iid()
adata = adata[:, :10].copy()
setup_anndata(adata)
model = LinearSCVI(adata, n_latent=10)
model.train(1, frequency=1, train_size=0.5)
assert len(model.history["elbo_train_set"]) == 2
assert len(model.history["elbo_test_set"]) == 2
model.get_loadings()
model.differential_expression(groupby="labels", group1="label_1")
model.differential_expression(groupby="labels", group1="label_1", group2="label_2")
def test_linear_scvi():
# test using raw
adata = synthetic_iid()
adata.raw = adata
adata = adata[:, :10].copy()
setup_anndata(adata, use_raw=True)
model = LinearSCVI(adata, n_latent=10)
model.train(1)
loadings = model.get_loadings()
pd.testing.assert_index_equal(loadings.index, adata.raw.var_names)
model.differential_expression(groupby="labels", group1="undefined_1")
model.differential_expression(groupby="labels",
group1="undefined_1",
group2="undefined_2")