def test_pca_transform(array_type):
A = array_type(A_list).astype('float32')
A_pca_abs = np.abs(A_pca)
A_svd_abs = np.abs(A_svd)
adata = AnnData(A)
sc.pp.pca(adata,
n_comps=4,
zero_center=True,
svd_solver='arpack',
dtype='float64')
assert np.linalg.norm(A_pca_abs[:, :4] -
np.abs(adata.obsm['X_pca'])) < 2e-05
sc.pp.pca(
adata,
n_comps=5,
zero_center=True,
svd_solver='randomized',
dtype='float64',
random_state=14,
)
assert np.linalg.norm(A_pca_abs - np.abs(adata.obsm['X_pca'])) < 2e-05
sc.pp.pca(adata,
n_comps=4,
zero_center=False,
dtype='float64',
random_state=14)
assert np.linalg.norm(A_svd_abs[:, :4] -
np.abs(adata.obsm['X_pca'])) < 2e-05
def test_pca_reproducible(pbmc3k_normalized, array_type, float_dtype):
pbmc = pbmc3k_normalized
pbmc.X = array_type(pbmc.X)
a = sc.pp.pca(pbmc, copy=True, dtype=float_dtype, random_state=42)
b = sc.pp.pca(pbmc, copy=True, dtype=float_dtype, random_state=42)
c = sc.pp.pca(pbmc, copy=True, dtype=float_dtype, random_state=0)
assert_equal(a, b)
# Test that changing random seed changes result
assert not np.array_equal(a.obsm["X_pca"], c.obsm["X_pca"])
def test_pca_reproducible(pbmc3k_normalized, array_type):
pbmc = pbmc3k_normalized
pbmc.X = array_type(pbmc.X)
a = sc.pp.pca(pbmc, copy=True, dtype=np.float64, random_state=42)
b = sc.pp.pca(pbmc, copy=True, dtype=np.float64, random_state=42)
c = sc.pp.pca(pbmc, copy=True, dtype=np.float64, random_state=0)
assert_equal(a, b)
# Test that changing random seed changes result
# Does not show up reliably with 32 bit computation
assert not np.array_equal(a.obsm["X_pca"], c.obsm["X_pca"])