def log10_heatmap(dna_samples,
dna_top_average_pathways,
dna_top_average_data,
data_type="pathways"):
merged_data = []
metadata_pathways = []
metadata_samples = []
if 'metadata' in vars and vars['metadata']:
merged_data, metadata_samples = utilities.merge_metadata(
vars['metadata'], dna_samples,
[[dna_top_average_pathways[i]] + dna_top_average_data[i]
for i in range(len(dna_top_average_pathways))])
metadata_pathways = [row.pop(0) for row in merged_data]
# get the metadata row numbers
metadata_rows = range(1, len(vars['metadata']))
document.show_hclust2(metadata_samples,
metadata_pathways,
merged_data,
title="Top " + str(max_sets) + " " + data_type +
" by average abundance",
metadata_rows=metadata_rows)
else:
document.show_hclust2(dna_samples,
dna_top_average_pathways,
dna_top_average_data,
title="Top " + str(max_sets) + " " + data_type +
" by average abundance")
return merged_data, metadata_pathways, metadata_samples
def test_merge_metadata_values_without_names(self):
""" Test the merge metadata function. Test values without names option."""
metadata = [["# samples", "s1", "s2"], ["feature1", "A", "B"],
["feature2", 1, 2]]
samples = ["s1", "s2"]
values = [[1, 2], [2, 4]]
merged, new_samples = utilities.merge_metadata(
metadata, samples, values, values_without_names=True)
expected = [["feature1", "A", "B"], ["feature2", 1, 2], [1, 2], [2, 4]]
expected_samples = ["s1", "s2"]
self.assertEqual(merged, expected)
self.assertEqual(new_samples, expected_samples)
def test_merge_metadata_reorder(self):
""" Test the merge metadata function. Test with reordering."""
metadata = [["# samples", "s1", "s2"], ["feature1", "A", "B"],
["feature2", 1, 2]]
samples = ["s2", "s1"]
values = [["bug1", 1, 2], ["bug2", 2, 4]]
merged, new_samples = utilities.merge_metadata(metadata, samples,
values)
expected = [["feature1", "A", "B"], ["feature2", 1, 2], ["bug1", 2, 1],
["bug2", 4, 2]]
expected_samples = ["s1", "s2"]
self.assertEqual(merged, expected)
self.assertEqual(new_samples, expected_samples)
def test_merge_metadata_nomatch(self):
""" Test the merge metadata function. Test with metadata not matching."""
metadata = [["# samples", "s3"], ["feature1", "A"], ["feature2", 1]]
samples = ["s1", "s2"]
values = [["bug1", 1, 2], ["bug2", 2, 4]]
# suppress warning message
# Redirect stdout
original_stdout = sys.stdout
sys.stdout = open(os.devnull, "w")
merged, new_samples = utilities.merge_metadata(metadata, samples,
values)
# Redirect stdout
sys.stdout = original_stdout
expected = [["bug1", 1, 2], ["bug2", 2, 4]]
self.assertEqual(merged, expected)
self.assertEqual(new_samples, samples)