def test_compute_ordination_correlation(self):
"""Functions correctly using valid input."""
# Defaults.
exp = (1.0, 0.0)
obs = compute_ordination_correlation(self.map1, self.coords1,
self.category1)
self.assertFloatEqual(obs[:2], exp)
self.assertIsProb(float(obs[2]))
# Spearman with second axis.
exp = (0.4, 0.6)
obs = compute_ordination_correlation(self.map1, self.coords1,
self.category1,
axis=2,
correlation_type='spearman')
self.assertFloatEqual(obs[:2], exp)
self.assertIsProb(float(obs[2]))
# No permutations.
exp = (1.0, 0.0, 'N/A')
obs = compute_ordination_correlation(self.map1, self.coords1,
self.category1,
num_permutations=0)
self.assertFloatEqual(obs, exp)
# Few permutations.
exp = (1.0, 0.0, 'Too few iters to compute p-value (num_iters=1)')
obs = compute_ordination_correlation(self.map1, self.coords1,
self.category1,
num_permutations=1)
self.assertEqual(obs, exp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
output_dir = opts.output_dir
create_dir(output_dir)
map_f = open(opts.map_fp, 'U')
coord_f = open(opts.coord_fp, 'U')
results = compute_ordination_correlation(map_f, coord_f, opts.category,
opts.axis, opts.type, opts.num_permutations)
header = ['Correlation coefficient', 'Parametric p-value',
'Nonparametric p-value']
with open(join(output_dir, 'ord_corr_results.txt'), 'w') as output_f:
output_f.write('\t'.join(header) + '\n')
output_f.write('%.4f\t%.4f\t%s\n' % results)
def test_compute_ordination_correlation_invalid_input(self):
"""Correctly handles invalid input."""
# category
with self.assertRaises(ValueError):
compute_ordination_correlation(self.map1, self.coords1, 'foo')
# category state
with self.assertRaises(ValueError):
compute_ordination_correlation(self.map1, self.coords1,
'Treatment')
# axis
with self.assertRaises(ValueError):
compute_ordination_correlation(self.map1, self.coords1,
self.category1, axis=-1)
with self.assertRaises(ValueError):
compute_ordination_correlation(self.map1, self.coords1,
self.category1, axis=4)
# correlation_type
with self.assertRaises(ValueError):
compute_ordination_correlation(self.map1, self.coords1,
self.category1,
correlation_type='foo')
# num_permutations
with self.assertRaises(ValueError):
compute_ordination_correlation(self.map1, self.coords1,
self.category1,
num_permutations=-1)
