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Updates to address reviewer comments
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@jwdebelius
jwdebelius committed Jan 19, 2016
1 parent 560dbdc commit 6c9b4a6
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Showing 2 changed files with 39 additions and 69 deletions.
51 changes: 20 additions & 31 deletions americangut/per_sample.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -281,11 +281,20 @@ def alpha_plot(opts, sample_ids):
sep='\t',
dtype=str,
)
alpha_map[['shannon_1k', 'PD_whole_tree_1k']] = \
alpha_map[['shannon_1k', 'PD_whole_tree_1k']].astype(float)
alpha_map.set_index('#SampleID', inplace=True)

results['index'] = alpha_map.index
alpha_metrics = ['shannon_1k', 'PD_whole_tree_1k']

# Checks the alpha_field is in the mapping file
for metric in alpha_metrics:
if metric not in alpha_map.columns:
raise ValueError('%s is not a valid alpha diversity field name.'
% metric)
# Checks the group_field is in the mapping file
if 'SIMPLE_BODY_SITE' not in alpha_map.columns:
raise ValueError('SIMPLE_BODY_SITE is not a valid field name.')

alpha_map[alpha_metrics] = alpha_map[alpha_metrics].astype(float)
alpha_map.set_index('#SampleID', inplace=True)

results = {}
for id_ in sample_ids:
Expand Down Expand Up @@ -587,9 +596,9 @@ def _plot_alpha(sample, alpha_map, alpha_field, group_field='SIMPLE_BODY_SITE',
----------
sample : str
The sample ID to be plotted
alpha_map_fp : str, dataframe
The filepath of a comma-seperated file or the pandas dataframe where
the sample ID are given in the `'#SampleID'` column, a column with
alpha_map_fp : pandas DataFrame
A pandas dataframe containing the sample metadata. The sample ID
should be given in the `'#SampleID'` column, a column with
the name given by `alpha_field` contains alpha diversity values,
and the `group_field` column specifying the groups which should be
used to seperate the data for making the distribution plot.
Expand All @@ -606,43 +615,23 @@ def _plot_alpha(sample, alpha_map, alpha_field, group_field='SIMPLE_BODY_SITE',
Returns
-------
If the sample is not included in the the mapping file, a string is returned
stating this fact.
If the sample is present, a matplotlib figure with the alpha diversity
distribution and a line indicating the sample value is returned.
distribution and a line indicating the sample value is returned. If a
file path is specified, the figure will be saved at the filepath instead
of returning.
If debug is passed, the following parameters are returned:
group : str
The value of the `group_field` for the sample
group_alpha : ndarray
The alpha diversity values assoicated with the group
The alpha diversity values associated with the group
sample_alpha : float
The alpha diversity for the sample
xlabel : str
The label used for the x-axis of the plot.
Raises
------
ValueError
If the alpha_field is not in alpha_map
ValueError
If the group_field is not in alpha_map
"""

# Checks the alpha_field is in the mapping file
if alpha_field not in alpha_map.columns:
raise ValueError('%s is not a valid alpha diversity field name.'
% alpha_field)
# Checks the group_field is in the mapping file
if group_field not in alpha_map.columns:
raise ValueError('%s is not a valid field name.' % group_field)
# Checks the same is in the mapping file
if sample not in alpha_map.index:
return ('%s does not have an alpha diversity value for %s.'
% (alpha_field, sample))

# Explicitly casts the alpha diversity to a float
alpha_map[alpha_field] = alpha_map[alpha_field].astype(float)

Expand Down
57 changes: 19 additions & 38 deletions tests/test_per_sample.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -266,46 +266,27 @@ def test_plot_alpha_no_sample(self):
alpha_field='alpha')
self.assertEqual(tvalue, kvalue)

def test_plot_alpha_alpha_field_error(self):
map_ = pd.DataFrame(
data=np.array([
['skin', '1990', 'female', 'Verity', 'US', 12.5],
['fecal', '1990', 'female', 'Verity', 'US', 8.6],
['fecal', '1987', 'male', 'Alex', 'US', 7.9],
['fecal', '1993', 'female', 'Annie', 'US', 7.5],
['skin', '1989', 'male', 'Dominic', 'UK', 14.0],
['fecal', '1986', 'female', 'Sarah', 'US', 15.0],
['oral', '1988', 'female', 'Shelby', 'AUS', 4.2],
]),
index=['VeP0', 'VeP1', 'AxP0', 'AnP0', 'DoD0', 'SaZ0', 'ShT0'],
columns=['SIMPLE_BODY_SITE', 'BIRTH_YEAR', 'SEX',
'HOST_SUBJECT_ID', 'NATIONALITY', 'alpha'],
)
def test_alpha_plts_metric_error_field_error(self):
opts = {'collapsed': {
'100nt': {
'alpha_map':
os.path.join(ag.WORKING_DIR.split('American-Gut')[0],
'American-Gut/tests/files/'
'test_mapping.txt')}},
'sample_type': 'fecal'}
with self.assertRaises(ValueError):
agps._plot_alpha(sample='VeP0',
alpha_map=map_,
alpha_field='InCryptid')

def test_plot_alpha_group_field_error(self):
map_ = pd.DataFrame(
data=np.array([
['skin', '1990', 'female', 'Verity', 'US', 12.5],
['fecal', '1990', 'female', 'Verity', 'US', 8.6],
['fecal', '1987', 'male', 'Alex', 'US', 7.9],
['fecal', '1993', 'female', 'Annie', 'US', 7.5],
['skin', '1989', 'male', 'Dominic', 'UK', 14.0],
['fecal', '1986', 'female', 'Sarah', 'US', 15.0],
['oral', '1988', 'female', 'Shelby', 'AUS', 4.2],
]),
index=['VeP0', 'VeP1', 'AxP0', 'AnP0', 'DoD0', 'SaZ0', 'ShT0'],
columns=['SIMPLE_BODY_SITE', 'BIRTH_YEAR', 'SEX',
'HOST_SUBJECT_ID', 'NATIONALITY', 'alpha'],
)
agps.alpha_plot(opts, ['sample_a', 'sample_b'])

def test_alpha_plot_group_field_error(self):
opts = {'collapsed': {
'100nt': {
'alpha_map':
os.path.join(ag.WORKING_DIR.split('American-Gut')[0],
'American-Gut/tests/files/'
'test_mapping_alpha.txt')}},
'sample_type': 'fecal'}
with self.assertRaises(ValueError):
agps._plot_alpha(sample='VeP0',
alpha_map=map_,
alpha_field='alpha',
group_field='BODY_HABITAT')
agps.alpha_plot(opts, ['sample_a', 'sample_b'])

if __name__ == '__main__':
main()

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