def test_beta_rarefaction_too_many_samples_dropped(self):
# mantel needs 3x3 or larger distance matrix
table = Table(np.array([[0, 1, 3], [1, 1, 2]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
with self.assertRaisesRegex(ValueError, '3x3 in size'):
beta_rarefaction(self.output_dir, table, 'braycurtis', 'upgma',
self.md, 2)
def test_beta_rarefaction_pearson_correlation(self):
beta_rarefaction(self.output_dir, self.table, 'jaccard', 'upgma',
self.md, 2, iterations=7, correlation_method='pearson'
)
self.assertBetaRarefactionValidity(
self.output_dir, 7, 'pearson', 'upgma')
def test_beta_rarefaction_with_phylogeny(self):
beta_rarefaction(self.output_dir, self.table,
'weighted_unifrac',
'upgma', self.md, 2, phylogeny=self.tree)
self.assertBetaRarefactionValidity(
self.output_dir, 10, 'spearman', 'upgma')
def test_beta_rarefaction_pearson_correlation(self):
beta_rarefaction(self.output_dir, self.table, 'jaccard', 'upgma',
self.md, 2, iterations=7, correlation_method='pearson'
)
self.assertBetaRarefactionValidity(
self.output_dir, 7, 'pearson', 'upgma')
def test_beta_rarefaction_too_many_samples_dropped(self):
# mantel needs 3x3 or larger distance matrix
table = Table(np.array([[0, 1, 3], [1, 1, 2]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
with self.assertRaisesRegex(ValueError, '3x3 in size'):
beta_rarefaction(self.output_dir, table, 'braycurtis', 'upgma',
self.md, 2)
def test_beta_rarefaction_minimum_iterations(self):
beta_rarefaction(self.output_dir,
self.table,
'braycurtis',
'upgma',
self.md,
2,
iterations=2)
self.assertBetaRarefactionValidity(self.output_dir, 2, 'spearman',
'upgma')
def test_beta_rarefaction_neighbor_joining(self):
beta_rarefaction(self.output_dir,
self.table,
'euclidean',
'nj',
self.md,
3,
iterations=5,
color_scheme='PiYG')
self.assertBetaRarefactionValidity(self.output_dir, 5, 'spearman',
'nj')
def test_beta_rarefaction_non_default_color_scheme(self):
beta_rarefaction(self.output_dir,
self.table,
'euclidean',
'upgma',
self.md,
3,
iterations=5,
color_scheme='PiYG')
self.assertBetaRarefactionValidity(self.output_dir, 5, 'spearman',
'upgma')
def test_beta_rarefaction_minimum_iterations(self):
beta_rarefaction(self.output_dir, self.table, 'braycurtis', 'upgma',
self.md, 2, iterations=2)
self.assertBetaRarefactionValidity(
self.output_dir, 2, 'spearman', 'upgma')
def test_beta_rarefaction_without_phylogeny(self):
beta_rarefaction(self.output_dir, self.table, 'braycurtis', 'upgma',
self.md, 2)
self.assertBetaRarefactionValidity(
self.output_dir, 10, 'spearman', 'upgma')
def test_beta_rarefaction_with_phylogeny(self):
beta_rarefaction(self.output_dir, self.table, 'weighted_unifrac',
'upgma', self.md, 2, phylogeny=self.tree)
self.assertBetaRarefactionValidity(
self.output_dir, 10, 'spearman', 'upgma')
def test_beta_rarefaction_empty_table(self):
table = Table(np.array([[]]), [], [])
with self.assertRaisesRegex(ValueError,
'shallow enough sampling depth'):
beta_rarefaction(self.output_dir, table, 'braycurtis', 'upgma',
self.md, 1)
def test_beta_rarefaction_empty_table(self):
table = Table(np.array([[]]), [], [])
with self.assertRaisesRegex(ValueError, 'feature table is empty'):
beta_rarefaction(self.output_dir, table, 'braycurtis', 'upgma',
self.md, 1)
def test_beta_rarefaction_without_phylogeny(self):
beta_rarefaction(self.output_dir, self.table, 'braycurtis', 'upgma',
self.md, 2)
self.assertBetaRarefactionValidity(
self.output_dir, 10, 'spearman', 'upgma')
def test_beta_rarefaction_non_default_color_scheme(self):
beta_rarefaction(self.output_dir, self.table, 'euclidean', 'upgma',
self.md, 3, iterations=5, color_scheme='PiYG')
self.assertBetaRarefactionValidity(
self.output_dir, 5, 'spearman', 'upgma')
def test_beta_rarefaction_neighbor_joining(self):
beta_rarefaction(self.output_dir, self.table, 'euclidean', 'nj',
self.md, 3, iterations=5, color_scheme='PiYG')
self.assertBetaRarefactionValidity(
self.output_dir, 5, 'spearman', 'nj')
def test_beta_rarefaction_all_samples_dropped(self):
with self.assertRaisesRegex(ValueError,
'shallow enough sampling depth'):
beta_rarefaction(self.output_dir, self.table, 'braycurtis',
'upgma', self.md, 100)
def test_beta_rarefaction_all_samples_dropped(self):
with self.assertRaisesRegex(ValueError,
'shallow enough sampling depth'):
beta_rarefaction(self.output_dir, self.table, 'braycurtis',
'upgma', self.md, 100)
def test_beta_rarefaction_missing_phylogeny(self):
with self.assertRaisesRegex(ValueError, 'Phylogeny must be provided'):
beta_rarefaction(self.output_dir, self.table,
'weighted_unifrac',
'upgma', self.md, 2)
def test_beta_rarefaction_missing_phylogeny(self):
with self.assertRaisesRegex(ValueError, 'Phylogeny must be provided'):
beta_rarefaction(self.output_dir, self.table, 'weighted_unifrac',
'upgma', self.md, 2)
def test_beta_rarefaction_empty_table(self):
table = Table(np.array([[]]), [], [])
with self.assertRaisesRegex(ValueError, 'feature table is empty'):
beta_rarefaction(self.output_dir, table, 'braycurtis', 'upgma',
self.md, 1)
