def test_run_within_atlas():
aname = 'Darmanis_2015'
atlas = AtlasFetcher().fetch_atlas(aname, kind='subsample')
matrix = atlas.copy()
cell_types = atlas.obs['CellType'].values
sa = Subsample(aname)
sa.fit(matrix)
# Small samples are a bit tricky, one cell can tip the balance
assert ((cell_types == sa.membership).mean() >= 0.85)
def test_run_across_atlas():
atlas = AtlasFetcher().fetch_atlas('Enge_2017', kind='subsample')
matrix = atlas.copy()
cell_types = atlas.obs['CellType'].values
sa = Subsample(
'Baron_2016',
n_pcs=25,
n_features_per_cell_type=3,
n_features_overdispersed=200,
)
sa.fit(matrix)
# Nobody's perfect
# Baron annotates Stellate cells more accurately, so we skip them
assert ((cell_types == sa.membership)[:60].mean() >= 0.5)