def test_taxa_file(self):
filtered_sample_ids, taxa_labels, collapsed_taxa_table = \
get_filtered_taxa_summary(TEST_MAPPING_FILE, TEST_TAXA_FILE,
self.metadata_category,
self.metadata_value,
select_taxa=self.taxa_ids)
# Make sure we only get out the matching sample
self.assertEqual(len(filtered_sample_ids), 1)
self.assertEqual(filtered_sample_ids[0], 'sample_a')
# Should get back our desired labels + "Others"
self.assertEqual(set(self.taxa_labels), set(taxa_labels))
# Should get the slide of the table corresponding to the matching
# sample
npt.assert_equal(collapsed_taxa_table, self.table[:, 0, None])
# Sample ticks to be labeled in the stack plot
if args.samples_file:
special_labels = get_sample_ids_to_label(args.samples_file)
else:
special_labels = []
# Specify taxa, otherwise the top N most abundant
if args.key_taxa_file:
select_taxa = get_key_taxa(args.key_taxa_file)
else:
select_taxa = None
filtered_sample_ids, taxa_labels, collapsed_taxa_table = \
get_filtered_taxa_summary(args.mapping_file, args.taxa_file,
args.metadata_category, args.metadata_value,
select_taxa=select_taxa)
colors = brewer2mpl.get_map('Spectral', 'Diverging',
len(taxa_labels)).mpl_colors
# Create stack plot
output = args.output_prefix + 'stack.' + args.output_type
make_stacked_plot(output, filtered_sample_ids, taxa_labels,
collapsed_taxa_table, args.ylabel, colors,
sample_ticks=special_labels)
# Create pie chart
output = args.output_prefix + 'pie.' + args.output_type
make_pie_chart(output, collapsed_taxa_table, colors)
