def test_format_title(self):
"""Tests converting string to title."""
self.assertEqual(format_title("observed_species"), "Observed Species")
self.assertEqual(format_title("chao1"), "Chao1")
self.assertEqual(format_title("shannon"), "Shannon")
# Test special mapping.
self.assertEqual(format_title("PD_whole_tree"), "Phylogenetic Diversity")
def _generate_alpha_diversity_boxplots(collated_adiv_dir, map_fp,
split_category, comparison_category,
rarefaction_depth, output_dir):
"""Generates per-body-site self vs. other alpha diversity boxplots.
Creates a plot for each input collated alpha diversity file (i.e. metric)
in collated_adiv_dir. Returns a list of plot filenames that were created in
output_dir.
Arguments:
collated_adiv_dir - path to directory containing one or more collated
alpha diversity files
map_fp - filepath to metadata mapping file
split_category - category to split on, e.g. body site. A boxplot will
be created for each category value (e.g. tongue, palm, etc.)
comparison_category - category to split on within each of the split
categories (e.g. self, other)
rarefaction_depth - rarefaction depth to use when pulling data from
rarefaction files
output_dir - directory to write output plot images to
"""
metadata_map = MetadataMap.parseMetadataMap(open(map_fp, 'U'))
collated_adiv_fps = glob(join(collated_adiv_dir, '*.txt'))
plot_title = 'Alpha diversity (%d seqs/sample)' % rarefaction_depth
# Generate a plot for each collated alpha diversity metric file.
created_files = []
for collated_adiv_fp in collated_adiv_fps:
adiv_metric = splitext(basename(collated_adiv_fp))[0]
x_tick_labels, dists = _collect_alpha_diversity_boxplot_data(
open(collated_adiv_fp, 'U'), metadata_map, rarefaction_depth,
split_category, comparison_category)
plot_figure = generate_box_plots(dists,
x_tick_labels=x_tick_labels,
title=plot_title,
x_label='Grouping',
y_label=format_title(adiv_metric))
plot_fp = join(output_dir, '%s.png' % adiv_metric)
plot_figure.savefig(plot_fp)
created_files.append(basename(plot_fp))
return created_files
