def test_make_distance_boxplots_suppress_plots(self):
"""Test correctly suppresses different plot types."""
obs = make_distance_boxplots(self.dm_f,
self.map_f, ['Bar'],
suppress_all_within=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 4)
self.assertEqual(len(obs[0][3]), 4)
self.assertEqual(obs[0][4], [None, None, None, None])
obs = make_distance_boxplots(self.dm_f,
self.map_f, ['Bar'],
suppress_all_within=True,
suppress_all_between=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 3)
self.assertEqual(len(obs[0][3]), 3)
self.assertEqual(obs[0][4], [None, None, None])
obs = make_distance_boxplots(self.dm_f,
self.map_f, ['Bar'],
suppress_all_within=True,
suppress_all_between=True,
suppress_individual_within=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 1)
self.assertEqual(len(obs[0][3]), 1)
self.assertEqual(obs[0][4], [None])
obs = make_distance_boxplots(self.dm_f,
self.map_f, ['Bar'],
suppress_all_within=True,
suppress_all_between=True,
suppress_individual_between=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 2)
self.assertEqual(len(obs[0][3]), 2)
self.assertEqual(obs[0][4], [None, None])
obs = make_distance_boxplots(self.dm_f,
self.map_f, ['Bar'],
suppress_individual_within=True,
suppress_individual_between=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 2)
self.assertEqual(len(obs[0][3]), 2)
self.assertEqual(obs[0][4], [None, None])
def test_make_distance_boxplots_box_color(self):
"""Test correctly colors boxes in a variety of ways."""
# Single box color for all.
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Bar'],
box_color='r')
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 5)
self.assertEqual(len(obs[0][3]), 5)
self.assertEqual(obs[0][4], ['r', 'r', 'r', 'r', 'r'])
# Single box color, with some plots suppressed.
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Bar'],
box_color='r',
suppress_individual_within=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 3)
self.assertEqual(len(obs[0][3]), 3)
self.assertEqual(obs[0][4], ['r', 'r', 'r'])
# Color individual within boxes.
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Foo'],
color_individual_within_by_field='Bar')
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Foo')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 7)
self.assertEqual(len(obs[0][3]), 7)
self.assertEqual(len(obs[0][4]), 7)
self.assertIsNone(obs[0][4][0])
self.assertIsNone(obs[0][4][1])
self.assertEqual(obs[0][4][2], (1.0, 0.0, 0.0))
self.assertEqual(obs[0][4][3], (0.0, 0.0, 1.0))
self.assertIsNone(obs[0][4][4])
self.assertIsNone(obs[0][4][5])
self.assertIsNone(obs[0][4][6])
# Color individual within boxes, make sure box_color is ignored.
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Foo'],
box_color='pink', color_individual_within_by_field='Bar')
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Foo')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 7)
self.assertEqual(len(obs[0][3]), 7)
self.assertEqual(len(obs[0][4]), 7)
self.assertIsNone(obs[0][4][0])
self.assertIsNone(obs[0][4][1])
self.assertEqual(obs[0][4][2], (1.0, 0.0, 0.0))
self.assertEqual(obs[0][4][3], (0.0, 0.0, 1.0))
self.assertIsNone(obs[0][4][4])
self.assertIsNone(obs[0][4][5])
self.assertIsNone(obs[0][4][6])
def test_make_distance_boxplots_box_color(self):
"""Test correctly colors boxes in a variety of ways."""
# Single box color for all.
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Bar'],
box_color='r')
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 5)
self.assertEqual(len(obs[0][3]), 5)
self.assertEqual(obs[0][4], ['r', 'r', 'r', 'r', 'r'])
# Single box color, with some plots suppressed.
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Bar'],
box_color='r',
suppress_individual_within=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 3)
self.assertEqual(len(obs[0][3]), 3)
self.assertEqual(obs[0][4], ['r', 'r', 'r'])
# Color individual within boxes.
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Foo'],
color_individual_within_by_field='Bar')
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Foo')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 7)
self.assertEqual(len(obs[0][3]), 7)
self.assertEqual(len(obs[0][4]), 7)
self.assertIsNone(obs[0][4][0])
self.assertIsNone(obs[0][4][1])
self.assertEqual(obs[0][4][2], (1.0, 0.0, 0.0))
self.assertEqual(obs[0][4][3], (0.0, 0.0, 1.0))
self.assertIsNone(obs[0][4][4])
self.assertIsNone(obs[0][4][5])
self.assertIsNone(obs[0][4][6])
# Color individual within boxes, make sure box_color is ignored.
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Foo'],
box_color='pink', color_individual_within_by_field='Bar')
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Foo')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 7)
self.assertEqual(len(obs[0][3]), 7)
self.assertEqual(len(obs[0][4]), 7)
self.assertIsNone(obs[0][4][0])
self.assertIsNone(obs[0][4][1])
self.assertEqual(obs[0][4][2], (1.0, 0.0, 0.0))
self.assertEqual(obs[0][4][3], (0.0, 0.0, 1.0))
self.assertIsNone(obs[0][4][4])
self.assertIsNone(obs[0][4][5])
self.assertIsNone(obs[0][4][6])
def test_make_distance_boxplots_suppress_plots(self):
"""Test correctly suppresses different plot types."""
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Bar'],
suppress_all_within=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 4)
self.assertEqual(len(obs[0][3]), 4)
self.assertEqual(obs[0][4], [None, None, None, None])
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Bar'],
suppress_all_within=True,
suppress_all_between=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 3)
self.assertEqual(len(obs[0][3]), 3)
self.assertEqual(obs[0][4], [None, None, None])
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Bar'],
suppress_all_within=True,
suppress_all_between=True,
suppress_individual_within=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 1)
self.assertEqual(len(obs[0][3]), 1)
self.assertEqual(obs[0][4], [None])
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Bar'],
suppress_all_within=True,
suppress_all_between=True,
suppress_individual_between=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 2)
self.assertEqual(len(obs[0][3]), 2)
self.assertEqual(obs[0][4], [None, None])
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Bar'],
suppress_individual_within=True,
suppress_individual_between=True)
self.assertEqual(len(obs), 1)
self.assertEqual(obs[0][0], 'Bar')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 2)
self.assertEqual(len(obs[0][3]), 2)
self.assertEqual(obs[0][4], [None, None])
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# Create the output dir if it doesn't already exist.
out_dir = opts.output_dir
try:
create_dir(out_dir)
except:
option_parser.error("Could not create or access output directory "
"specified with the -o option.")
map_f = open(opts.mapping_fp, 'U')
dm_f = open(opts.distance_matrix_fp, 'U')
fields = map(strip, opts.fields.split(','))
fields = [field.strip('"').strip("'") for field in fields]
color_individual_within_by_field = opts.color_individual_within_by_field
results = make_distance_boxplots(dm_f, map_f, fields, width=opts.width,
height=opts.height, suppress_all_within=opts.suppress_all_within,
suppress_all_between=opts.suppress_all_between,
suppress_individual_within=opts.suppress_individual_within,
suppress_individual_between=opts.suppress_individual_between,
y_min=opts.y_min, y_max=opts.y_max,
whisker_length=opts.whisker_length, box_width=opts.box_width,
box_color=opts.box_color,
color_individual_within_by_field=color_individual_within_by_field,
sort=opts.sort)
for field, plot_figure, plot_data, plot_labels, plot_colors in results:
output_plot_fp = join(out_dir, "%s_Distances.%s" %
(field, opts.imagetype))
plot_figure.savefig(output_plot_fp, format=opts.imagetype,
transparent=opts.transparent)
if not opts.suppress_significance_tests:
sig_tests_f = open(join(out_dir, "%s_Stats.txt" % field), 'w')
sig_tests_results = all_pairs_t_test(plot_labels, plot_data,
tail_type=opts.tail_type,
num_permutations=opts.num_permutations)
sig_tests_f.write(sig_tests_results)
sig_tests_f.close()
if opts.save_raw_data:
# Write the raw plot data into a tab-delimited file.
assert(len(plot_labels) == len(plot_data))
raw_data_fp = join(out_dir, "%s_Distances.txt" % field)
raw_data_f = open(raw_data_fp, 'w')
for label, data in zip(plot_labels, plot_data):
raw_data_f.write(label.replace(" ", "_") + "\t")
raw_data_f.write("\t".join(map(str, data)))
raw_data_f.write("\n")
raw_data_f.close()
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# Create the output dir if it doesn't already exist.
out_dir = opts.output_dir
try:
create_dir(out_dir)
except:
option_parser.error("Could not create or access output directory "
"specified with the -o option.")
map_f = open(opts.mapping_fp, 'U')
dm_f = open(opts.distance_matrix_fp, 'U')
fields = map(strip, opts.fields.split(','))
fields = [field.strip('"').strip("'") for field in fields]
color_individual_within_by_field = opts.color_individual_within_by_field
results = make_distance_boxplots(dm_f, map_f, fields, width=opts.width,
height=opts.height, suppress_all_within=opts.suppress_all_within,
suppress_all_between=opts.suppress_all_between,
suppress_individual_within=opts.suppress_individual_within,
suppress_individual_between=opts.suppress_individual_between,
y_min=opts.y_min, y_max=opts.y_max,
whisker_length=opts.whisker_length, box_width=opts.box_width,
box_color=opts.box_color,
color_individual_within_by_field=color_individual_within_by_field,
sort=opts.sort)
for field, plot_figure, plot_data, plot_labels, plot_colors in results:
output_plot_fp = join(out_dir, "%s_Distances.%s" %
(field, opts.imagetype))
plot_figure.savefig(output_plot_fp, format=opts.imagetype,
transparent=opts.transparent)
if not opts.suppress_significance_tests:
sig_tests_f = open(join(out_dir, "%s_Stats.txt" % field), 'w')
sig_tests_results = all_pairs_t_test(plot_labels, plot_data,
tail_type=opts.tail_type,
num_permutations=opts.num_permutations)
sig_tests_f.write(sig_tests_results)
sig_tests_f.close()
if opts.save_raw_data:
# Write the raw plot data into a tab-delimited file.
assert(len(plot_labels) == len(plot_data))
raw_data_fp = join(out_dir, "%s_Distances.txt" % field)
raw_data_f = open(raw_data_fp, 'w')
for label, data in zip(plot_labels, plot_data):
raw_data_f.write(label.replace(" ", "_") + "\t")
raw_data_f.write("\t".join(map(str, data)))
raw_data_f.write("\n")
raw_data_f.close()
def test_make_distance_boxplots(self):
"""Test correctly generates plot, raw data, and labels."""
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Foo', 'Bar'])
self.assertEqual(len(obs), 2)
self.assertEqual(obs[0][0], 'Foo')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 7)
self.assertEqual(len(obs[0][3]), 7)
self.assertEqual(obs[0][4], [None, None, None, None, None, None, None])
self.assertEqual(obs[1][0], 'Bar')
self.assertTrue(isinstance(obs[1][1], Figure))
self.assertEqual(len(obs[1][2]), 5)
self.assertEqual(len(obs[1][3]), 5)
self.assertEqual(obs[1][4], [None, None, None, None, None])
def test_make_distance_boxplots(self):
"""Test correctly generates plot, raw data, and labels."""
obs = make_distance_boxplots(self.dm_f, self.map_f, ['Foo', 'Bar'])
self.assertEqual(len(obs), 2)
self.assertEqual(obs[0][0], 'Foo')
self.assertTrue(isinstance(obs[0][1], Figure))
self.assertEqual(len(obs[0][2]), 7)
self.assertEqual(len(obs[0][3]), 7)
self.assertEqual(obs[0][4], [None, None, None, None, None, None, None])
self.assertEqual(obs[1][0], 'Bar')
self.assertTrue(isinstance(obs[1][1], Figure))
self.assertEqual(len(obs[1][2]), 5)
self.assertEqual(len(obs[1][3]), 5)
self.assertEqual(obs[1][4], [None, None, None, None, None])