def test_multiple_metrics(self):
t = biom.Table(np.array([[150, 100, 100], [50, 100, 100]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
obs = _compute_rarefaction_data(feature_table=t,
min_depth=1,
max_depth=200,
steps=2,
iterations=1,
phylogeny=None,
metrics=['observed_features',
'shannon'])
exp_ind = pd.MultiIndex.from_product(
[[1, 200], [1]],
names=['_alpha_rarefaction_depth_column_', 'iter'])
exp = pd.DataFrame(data=[[1, 2], [1, 2], [1, 2]],
columns=exp_ind,
index=['S1', 'S2', 'S3'])
pdt.assert_frame_equal(obs['observed_features'], exp)
exp = pd.DataFrame(data=[[0., 0.811278124459], [0., 1.], [0., 1.]],
columns=exp_ind,
index=['S1', 'S2', 'S3'])
pdt.assert_frame_equal(obs['shannon'], exp)
def test_faith_pd(self):
t = biom.Table(np.array([[150, 100, 100], [50, 100, 100]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
p = skbio.TreeNode.read(
io.StringIO('((O1:0.25, O2:0.50):0.25, O3:0.75)root;'))
obs = _compute_rarefaction_data(feature_table=t,
min_depth=1,
max_depth=200,
steps=2,
iterations=1,
phylogeny=p,
metrics=['faith_pd'])
self.assertTrue('faith_pd' in obs)
def test_faith_pd(self):
t = biom.Table(np.array([[150, 100, 100], [50, 100, 100]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
p = skbio.TreeNode.read(io.StringIO(
'((O1:0.25, O2:0.50):0.25, O3:0.75)root;'))
obs = _compute_rarefaction_data(feature_table=t,
min_depth=1,
max_depth=200,
steps=2,
iterations=1,
phylogeny=p,
metrics=['faith_pd'])
self.assertTrue('faith_pd' in obs)
def test_observed_otus(self):
t = biom.Table(np.array([[150, 100, 100], [50, 100, 100]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
obs = _compute_rarefaction_data(feature_table=t,
min_depth=1,
max_depth=200,
steps=2,
iterations=1,
phylogeny=None,
metrics=['observed_otus'])
exp_ind = pd.MultiIndex.from_product([[1, 200], [1]],
names=['depth', 'iter'])
exp = pd.DataFrame(data=[[1, 2], [1, 2], [1, 2]],
columns=exp_ind,
index=['S1', 'S2', 'S3'])
pdt.assert_frame_equal(obs['observed_otus'], exp)
def test_observed_otus(self):
t = biom.Table(np.array([[150, 100, 100], [50, 100, 100]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
obs = _compute_rarefaction_data(feature_table=t,
min_depth=1,
max_depth=200,
steps=2,
iterations=1,
phylogeny=None,
metrics=['observed_otus'])
exp_ind = pd.MultiIndex.from_product(
[[1, 200], [1]],
names=['depth', 'iter'])
exp = pd.DataFrame(data=[[1, 2], [1, 2], [1, 2]],
columns=exp_ind,
index=['S1', 'S2', 'S3'])
pdt.assert_frame_equal(obs['observed_otus'], exp)