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import numpy as np | ||
import pandas as pd | ||
from scipy.sparse import csr_matrix | ||
from scipy.stats import norm | ||
from anndata import AnnData | ||
from numpy.testing import assert_almost_equal | ||
from ..method_zscore import zscore, run_zscore | ||
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def test_zscore(): | ||
m = csr_matrix(np.array([[-7., -1., 1., 1.], [-4., -2., 1., 2.], [1., 2., 5., 1.], [1., 1., 6., 2.]], dtype=np.float32)) | ||
m = np.array([[-7., -1., 1., 1.], [-4., -2., 1., 2.], [1., 2., 5., 1.], [1., 1., 6., 2.], [-8., -7., 1., 1.]], dtype=np.float32) | ||
net = np.array([[1., 0.], [1, 0.], [0., -1.], [0., -1.]], dtype=np.float32) | ||
act, pvl = zscore(m, net) | ||
assert act[0, 0] < 0 | ||
assert act[1, 0] < 0 | ||
assert act[2, 0] > 0 | ||
assert act[3, 0] > 0 | ||
assert act[4, 0] < 0 | ||
assert np.all((0. <= pvl) * (pvl <= 1.)) | ||
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act2, pvl2 = zscore(m, net, flavor='KSEA') | ||
assert act2[0, 0] < 0 | ||
assert act2[1, 0] < 0 | ||
assert act2[2, 0] < 0 | ||
assert act2[3, 0] < 0 | ||
assert act2[4, 0] < 0 | ||
assert np.all((0. <= pvl2) * (pvl2 <= 1.)) | ||
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def test_run_zscore(): | ||
m = np.array([[7., 1., 1., 1.], [4., 2., 1., 2.], [1., 2., 5., 1.], [1., 1., 6., 2.]]) | ||
m = np.array([[-7., -1., 1., 1.], [-4., -2., 1., 2.], [1., 2., 5., 1.], [1., 1., -6., -8.], [-8., -7., 1., 1.]]) | ||
r = np.array(['S1', 'S2', 'S3', 'S4']) | ||
c = np.array(['G1', 'G2', 'G3', 'G4']) | ||
df = pd.DataFrame(m, index=r, columns=c) | ||
net = pd.DataFrame([['T1', 'G1', 1], ['T1', 'G2', 2], ['T2', 'G3', -3], ['T2', 'G4', 4]], | ||
net = pd.DataFrame([['T1', 'G1', 1], ['T1', 'G2', 1], ['T2', 'G3', -1], ['T2', 'G4', -1]], | ||
columns=['source', 'target', 'weight']) | ||
res = run_zscore(df, net, verbose=True, use_raw=False, min_n=0) | ||
assert res[0].loc['S1', 'T2'] > 0 | ||
assert res[0].loc['S1', 'T2'] < 0 | ||
assert res[0].loc['S2', 'T2'] < 0 | ||
assert res[0].loc['S3', 'T2'] > 0 | ||
assert res[0].loc['S3', 'T2'] < 0 | ||
assert res[0].loc['S4', 'T2'] > 0 | ||
assert res[1].map(lambda x: 0 <= x <= 1).all().all() | ||
assert res[0].loc['S5', 'T2'] < 0 | ||
assert res[1].map(lambda x: 0 <= x <= 1).all().all() | ||
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res2 = run_zscore(df, net, verbose=True, use_raw=False, min_n=0, flavor='KSEA') | ||
assert res2[0].loc['S1', 'T2'] > 0 | ||
assert res2[0].loc['S2', 'T2'] < 0 | ||
assert res2[0].loc['S3', 'T2'] < 0 | ||
assert res2[0].loc['S4', 'T2'] > 0 | ||
assert res2[0].loc['S5', 'T2'] > 0 | ||
assert res2[1].map(lambda x: 0 <= x <= 1).all().all() | ||
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adata = AnnData(df.astype(np.float32)) | ||
run_zscore(adata, net, verbose=True, use_raw=False, min_n=0) |