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test_core.py
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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, emperor development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.md, distributed with this software.
# ----------------------------------------------------------------------------
from __future__ import division
from unittest import TestCase, main
from copy import deepcopy
from os.path import exists
from shutil import rmtree
from io import StringIO
from skbio import OrdinationResults
from jinja2 import Template
import warnings
import pandas as pd
import numpy as np
from emperor.core import Emperor
from emperor.util import EmperorWarning
# account for what's allowed in python 2 vs PY3K
try:
from . import _test_core_strings as tcs
except Exception:
import _test_core_strings as tcs
class TopLevelTests(TestCase):
def setUp(self):
self.maxDiff = None
or_f = StringIO(tcs.PCOA_STRING)
self.ord_res = OrdinationResults.read(or_f)
eigvals = self.ord_res.eigvals
samples = self.ord_res.samples
props = self.ord_res.proportion_explained
# make modified copies of the ordinations
a = OrdinationResults(eigvals=eigvals.copy(),
samples=np.abs(samples).copy(),
proportion_explained=props.copy(),
short_method_name='PCoA',
long_method_name='Princpal Coordinates Analysis')
b = OrdinationResults(eigvals=eigvals.copy(),
samples=np.sin(samples).copy(),
proportion_explained=props.copy(),
short_method_name='PCoA',
long_method_name='Princpal Coordinates Analysis')
c = OrdinationResults(eigvals=eigvals.copy(),
samples=np.cos(samples.copy()),
proportion_explained=props.copy(),
short_method_name='PCoA',
long_method_name='Princpal Coordinates Analysis')
# biplot ordination with 5 features
features = np.abs(samples / 2.0).copy()[:5]
features.index = 'f.' + features.index
biplot_scores = np.ones((9, 5))
d = OrdinationResults(eigvals=eigvals.copy(),
samples=samples.copy(),
features=features,
biplot_scores=biplot_scores,
proportion_explained=props.copy(),
short_method_name='RDA',
long_method_name='Redundancy Analysis')
self.biplot = d
feature_mf = pd.DataFrame(index=['f.PC.636', 'f.PC.635', 'f.PC.356',
'f.PC.481', 'f.PC.354'])
feature_mf['Category'] = ['foo', 'bar', 'baz', 'foo', 'foo']
feature_mf['Second'] = ['No', 'Yes', 'Noes', 'Noooo', 'Yep']
self.feature_mf = feature_mf
self.jackknifed = [a, b, c]
data = \
[['PC.354', 'Control', '20061218', 'Ctrol_mouse_I.D._354'],
['PC.355', 'Control', '20061218', 'Control_mouse_I.D._355'],
['PC.356', 'Control', '20061126', 'Control_mouse_I.D._356'],
['PC.481', 'Control', '20070314', 'Control_mouse_I.D._481'],
['PC.593', 'Control', '20071210', 'Control_mouse_I.D._593'],
['PC.607', 'Fast', '20071112', 'Fasting_mouse_I.D._607'],
['PC.634', 'Fast', '20080116', 'Fasting_mouse_I.D._634'],
['PC.635', 'Fast', '20080116', 'Fasting_mouse_I.D._635'],
['PC.636', 'Fast', '20080116', 'Fasting_mouse_I.D._636']]
headers = ['SampleID', 'Treatment', 'DOB', 'Description']
self.mf = pd.DataFrame(data=data, columns=headers)
self.mf.set_index('SampleID', inplace=True)
self.files_to_remove = []
# note that we don't test with remote=True because the url is resolved
# by emperor.util.resolve_stable_url, so it is bound to change
# depending on the environment executing the test
self.url = ('https://cdn.rawgit.com/biocore/emperor/new-api/emperor/'
'support_files')
self.expected_metadata = [['PC.636', 'Fast', '20080116',
'Fasting_mouse_I.D._636'],
['PC.635', 'Fast', '20080116',
'Fasting_mouse_I.D._635'],
['PC.356', 'Control', '20061126',
'Control_mouse_I.D._356'],
['PC.481', 'Control', '20070314',
'Control_mouse_I.D._481'],
['PC.354', 'Control', '20061218',
'Ctrol_mouse_I.D._354'],
['PC.593', 'Control', '20071210',
'Control_mouse_I.D._593'],
['PC.355', 'Control', '20061218',
'Control_mouse_I.D._355'],
['PC.607', 'Fast', '20071112',
'Fasting_mouse_I.D._607'],
['PC.634', 'Fast', '20080116',
'Fasting_mouse_I.D._634']]
self.expected_coords = [[-0.65199581, -0.3417785, 0.15713116,
-0.15964022, 0.415116],
[-0.5603277, 0.10857736, -0.32567899,
0.37501378, -0.58348783],
[0.53948353, -0.30683242, -0.67700431,
0.2038205, 0.10443355],
[0.09964195, -0.03293232, 0.14978637,
-0.81603885, -0.30134308],
[0.66108924, -0.01417628, 0.05537096,
-0.11036488, -0.34569241],
[0.54903768, 0.32957521, 0.76122421,
0.43227217, 0.0482525],
[0.40202459, -0.45765549, -0.07284389,
0.04670223, 0.36567513],
[-0.21532605, 1., -0.31976502, -0.13561209,
0.35686552],
[-0.82362744, -0.28477756, 0.27177951,
0.16384737, -0.05981938]]
self.expected_biplot_coords = [
[0.7989764321707692, 0.41882625725119405, 0.19255353093594343,
0.19562821395993216, 0.5086963730424037],
[0.6866434036312, 0.1330541540144393, 0.39909740671082994,
0.45955382957848684, 0.7150245690992273],
[0.6611002961979922, 0.37600222318672283, 0.8296226448056473,
0.24976813456784003, 0.12797619689815815],
[0.12210441648907923, 0.04035631834856271, 0.18355298799796177,
1.0, 0.3692754065598425],
[0.8101198147298804, 0.01737206462987538, 0.06785333685041521,
0.135244634257307, 0.4236224898810244]]
np.random.seed(111)
def tearDown(self):
for path in self.files_to_remove:
if exists(path):
rmtree(path)
def test_plot_width_and_height(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
emp.width = '111px'
emp.height = '111px'
self.assertEqual(emp.width, '111px')
self.assertEqual(emp.height, '111px')
def test_initial(self):
emp = Emperor(self.ord_res, self.mf, remote=self.url)
self.assertEqual(emp.width, '100%')
self.assertEqual(emp.height, '500px')
self.assertEqual(emp.settings, {})
self.assertEqual(emp.base_url, 'https://cdn.rawgit.com/biocore/emperor'
'/new-api/emperor/support_files')
self.assertEqual(emp.jackknifed, [])
self.assertEqual(emp.procrustes, [])
self.assertEqual(emp.procrustes_names, [])
self.assertEqual(emp.custom_axes, [])
self.assertEqual(emp.jackknifing_method, 'IQR')
emp.jackknifing_method = 'sdev'
self.assertEqual(emp.jackknifing_method, 'sdev')
def test_initial_biplots(self):
emp = Emperor(self.biplot, self.mf, self.feature_mf, remote=self.url)
self.assertEqual(emp.width, '100%')
self.assertEqual(emp.height, '500px')
self.assertEqual(emp.settings, {})
self.assertEqual(emp.jackknifed, [])
self.assertEqual(emp.procrustes, [])
self.assertEqual(emp.procrustes_names, [])
self.assertEqual(emp.custom_axes, [])
self.assertEqual(emp.jackknifing_method, 'IQR')
feature_mf = pd.DataFrame(index=['f.PC.636', 'f.PC.635', 'f.PC.356',
'f.PC.481', 'f.PC.354'])
feature_mf['Category'] = ['foo', 'bar', 'baz', 'foo', 'foo']
feature_mf['Second'] = ['No', 'Yes', 'Noes', 'Noooo', 'Yep']
# it is redundant, but the mapping file should remain untouched
pd.util.testing.assert_frame_equal(feature_mf, emp.feature_mf,
check_names=False)
self.assertEqual(emp.base_url, 'https://cdn.rawgit.com/biocore/emperor'
'/new-api/emperor/support_files')
def test_initial_biplots_no_metadata(self):
emp = Emperor(self.biplot, self.mf, remote=self.url)
self.assertEqual(emp.width, '100%')
self.assertEqual(emp.height, '500px')
self.assertEqual(emp.settings, {})
self.assertEqual(emp.jackknifed, [])
self.assertEqual(emp.procrustes, [])
self.assertEqual(emp.procrustes_names, [])
empty_mf = pd.DataFrame(index=['f.PC.636', 'f.PC.635', 'f.PC.356',
'f.PC.481', 'f.PC.354'])
empty_mf['all'] = 'All elements'
pd.util.testing.assert_frame_equal(empty_mf, emp.feature_mf,
check_names=False)
self.assertEqual(emp.base_url, 'https://cdn.rawgit.com/biocore/emperor'
'/new-api/emperor/support_files')
def test_one_dimensional(self):
self.ord_res.samples = self.ord_res.samples.iloc[:, :1].copy()
self.ord_res.eigvals = self.ord_res.eigvals.iloc[:1].copy()
self.ord_res.proportion_explained = \
self.ord_res.proportion_explained[:1].copy()
with self.assertRaisesRegexp(ValueError, "Ordinations with less than "
"two dimensions are not supported"):
Emperor(self.ord_res, self.mf, remote=False)
def test_initial_unbalanced_more_than_five(self):
mf = self.mf.copy()
mf.drop(['PC.354', 'PC.355', 'PC.356', 'PC.481', 'PC.607', 'PC.636'],
inplace=True)
with self.assertRaisesRegexp(KeyError, "There are samples not "
"included in the sample mapping file. "
"Override this error by using the "
"`ignore_missing_samples` argument. "
"Showing only the first 5 samples out of "
"6: PC.354, PC.355, PC.356, PC.481, "
"PC.607 ..."):
Emperor(self.ord_res, mf, remote=self.url)
def test_initial_unbalanced(self):
mf = self.mf.copy()
mf.drop(['PC.354'], inplace=True)
with self.assertRaisesRegexp(KeyError, "There are samples not "
"included in the sample mapping file. "
"Override this error by using the "
"`ignore_missing_samples` argument. "
"Offending samples: PC.354"):
Emperor(self.ord_res, mf, remote=self.url)
# test feature metadata
fmf = self.feature_mf.copy()
fmf.drop(['f.PC.636'], inplace=True)
with self.assertRaisesRegexp(KeyError, "There are features not "
"included in the feature mapping file. "
"Override this error by using the "
"`ignore_missing_samples` argument. "
"Offending features: f.PC.636"):
Emperor(self.biplot, self.mf, fmf, remote=self.url)
def test_initial_unbalanced_ignore(self):
expected = self.mf.copy()
mf = self.mf.copy()
mf.drop(['PC.634'], inplace=True)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
emp = Emperor(self.ord_res, mf, remote=self.url,
ignore_missing_samples=True)
self.assertTrue(len(w) == 1)
self.assertTrue(issubclass(w[-1].category, EmperorWarning))
self.assertEqual("1 out of 9 samples have no metadata and are "
"being included with a placeholder value.",
str(w[-1].message))
expected.loc['PC.634'] = ['This element has no metadata'] * 3
pd.util.testing.assert_frame_equal(expected.sort_index(),
emp.mf.sort_index(),
check_names=False)
expected = self.feature_mf.copy()
fmf = self.feature_mf.copy()
fmf.drop(['f.PC.636'], inplace=True)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
emp = Emperor(self.biplot, self.mf, fmf, remote=self.url,
ignore_missing_samples=True)
self.assertTrue(len(w) == 1)
self.assertTrue(issubclass(w[-1].category, EmperorWarning))
self.assertEqual("1 out of 5 features have no metadata and are "
"being included with a placeholder value.",
str(w[-1].message))
expected.loc['f.PC.636'] = ['This element has no metadata'] * 2
pd.util.testing.assert_frame_equal(expected.sort_index(),
emp.feature_mf.sort_index(),
check_names=False)
def test_no_overlap(self):
mf = self.mf.copy()
mf.index = mf.index + '.not'
with self.assertRaisesRegexp(ValueError, 'None of the sample '
'identifiers match between the metadata '
'and the coordinates. Verify that you are'
' using metadata and coordinates '
'corresponding to the same dataset.'):
Emperor(self.ord_res, mf, remote=self.url)
fmf = self.feature_mf.copy()
fmf.index = fmf.index + '.not'
with self.assertRaisesRegexp(ValueError, 'None of the feature '
'identifiers match between the metadata '
'and the coordinates. Verify that you are'
' using metadata and coordinates '
'corresponding to the same dataset.'):
Emperor(self.biplot, self.mf, fmf, remote=self.url)
def test_get_template(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
obs = emp._get_template(False)
self.assertTrue(isinstance(obs, Template))
self.assertTrue(obs.filename.endswith('/jupyter-template.html'))
def test_render_style(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
obs = emp.render_style()
self.assertEqual(tcs.STYLE_STRING, obs)
def test_render_html(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
obs = emp.render_html('emperor-notebook-0x9cb72f54')
self.assertEqual(tcs.DIV_STRING, obs)
def test_render_base_dependencies(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
obs = emp.render_base_dependencies()
self.assertEqual(tcs.DEPS_STRING, obs)
def test_render_js(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
emp.js_on_ready = "console.log('Hello from the other side');"
obs = emp.render_js('emperor-notebook-0x9cb72f54')
self.assertEqual(tcs.JS_STRING, obs)
def test_get_template_standalone(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
obs = emp._get_template(True)
self.assertTrue(isinstance(obs, Template))
self.assertTrue(obs.filename.endswith('/standalone-template.html'))
def test_formatting(self):
emp = Emperor(self.ord_res, self.mf, remote=self.url)
obs = str(emp)
self.assertEqual(tcs.HTML_STRING, obs)
def test_formatting_standalone(self):
local_path = './some-local-path/'
emp = Emperor(self.ord_res, self.mf, remote=local_path)
self.assertEqual(emp.base_url, local_path)
obs = emp.make_emperor(standalone=True)
self.assertEqual(tcs.STANDALONE_HTML_STRING, obs)
def test_remote_url(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
self.assertEqual(emp.base_url, "/nbextensions/emperor/support_files")
def test_remote_url_custom(self):
emp = Emperor(self.ord_res, self.mf, remote='/foobersurus/bar/')
self.assertEqual(emp.base_url, '/foobersurus/bar/')
def test_unnamed_index(self):
self.mf.index.name = None
emp = Emperor(self.ord_res, self.mf, remote=self.url)
obs = str(emp)
self.assertEqual(tcs.HTML_STRING, obs)
def test_copy_support_files_use_base(self):
local_path = './some-local-path/'
emp = Emperor(self.ord_res, self.mf, remote=local_path)
self.assertEqual(emp.base_url, local_path)
emp.copy_support_files()
self.assertTrue(exists(local_path))
self.files_to_remove.append(local_path)
def test_copy_support_files_use_target(self):
local_path = './some-local-path/'
emp = Emperor(self.ord_res, self.mf, remote=local_path)
self.assertEqual(emp.base_url, local_path)
emp.copy_support_files(target='./something-else')
self.assertTrue(exists('./something-else'))
self.files_to_remove.append(local_path)
self.files_to_remove.append('./something-else')
def test_process_data(self):
emp = Emperor(self.ord_res, self.mf, remote=self.url)
(coord_ids, coords, pct_var, ci, headers, metadata, names,
edges,
bi_coords, bi_ids,
bi_headers, bi_metadata) = emp._process_data([], 'IQR')
self.assertEqual(coord_ids, ['PC.636', 'PC.635', 'PC.356', 'PC.481',
'PC.354', 'PC.593', 'PC.355', 'PC.607', 'PC.634'])
np.testing.assert_array_almost_equal(coords, self.expected_coords)
obs_pct_var = np.array([26.688705, 16.25637, 13.775413, 11.217216,
10.024775])
np.testing.assert_array_almost_equal(pct_var, obs_pct_var)
np.testing.assert_array_almost_equal(ci, [])
self.assertEqual(headers, ['SampleID', 'Treatment', 'DOB',
'Description'])
self.assertEqual(metadata, self.expected_metadata)
self.assertEqual(names, [0, 1, 2, 3, 4])
self.assertEqual(edges, [])
self.assertTrue(bi_coords is None)
self.assertTrue(bi_ids is None)
self.assertTrue(bi_headers is None)
self.assertTrue(bi_metadata is None)
def test_process_data_issue_700(self):
self.mf.drop(['Treatment', 'DOB', 'Description'], axis=1, inplace=True)
emp = Emperor(self.ord_res, self.mf, remote=self.url)
(coord_ids, coords, pct_var, ci, headers, metadata, names,
edges,
bi_coords, bi_ids,
bi_headers, bi_metadata) = emp._process_data([], 'IQR')
self.assertEqual(coord_ids, ['PC.636', 'PC.635', 'PC.356', 'PC.481',
'PC.354', 'PC.593', 'PC.355', 'PC.607', 'PC.634'])
np.testing.assert_array_almost_equal(coords, self.expected_coords)
obs_pct_var = np.array([26.688705, 16.25637, 13.775413, 11.217216,
10.024775])
np.testing.assert_array_almost_equal(pct_var, obs_pct_var)
np.testing.assert_array_almost_equal(ci, [])
self.assertEqual(headers, ['SampleID'])
ids = ['PC.636', 'PC.635', 'PC.356', 'PC.481', 'PC.354', 'PC.593',
'PC.355', 'PC.607', 'PC.634']
self.assertEqual(metadata, [[i] for i in ids])
self.assertEqual(names, [0, 1, 2, 3, 4])
self.assertEqual(edges, [])
self.assertTrue(bi_coords is None)
self.assertTrue(bi_ids is None)
self.assertTrue(bi_headers is None)
self.assertTrue(bi_metadata is None)
def test_process_data_biplots(self):
emp = Emperor(self.biplot, self.mf, self.feature_mf, remote=self.url)
(coord_ids, coords, pct_var, ci, headers, metadata, names,
edges,
bi_coords, bi_ids,
bi_headers, bi_metadata) = emp._process_data([], 'IQR')
self.assertEqual(coord_ids, ['PC.636', 'PC.635', 'PC.356', 'PC.481',
'PC.354', 'PC.593', 'PC.355', 'PC.607', 'PC.634'])
np.testing.assert_array_almost_equal(coords, self.expected_coords)
obs_pct_var = np.array([26.688705, 16.25637, 13.775413, 11.217216,
10.024775])
np.testing.assert_array_almost_equal(pct_var, obs_pct_var)
np.testing.assert_array_almost_equal(ci, [])
self.assertEqual(headers, ['SampleID', 'Treatment', 'DOB',
'Description'])
self.assertEqual(metadata, self.expected_metadata)
self.assertEqual(names, [0, 1, 2, 3, 4])
self.assertEqual(edges, [])
np.testing.assert_array_almost_equal(bi_coords,
self.expected_biplot_coords)
self.assertEqual(bi_ids, ['f.PC.636', 'f.PC.635', 'f.PC.356',
'f.PC.481', 'f.PC.354'])
self.assertEqual(bi_headers, ['SampleID', 'Category', 'Second'])
self.assertEqual(bi_metadata, [['f.PC.636', 'foo', 'No'],
['f.PC.635', 'bar', 'Yes'],
['f.PC.356', 'baz', 'Noes'],
['f.PC.481', 'foo', 'Noooo'],
['f.PC.354', 'foo', 'Yep']])
def test_process_data_biplots_no_metadata(self):
emp = Emperor(self.biplot, self.mf, remote=self.url)
(coord_ids, coords, pct_var, ci, headers, metadata, names,
edges,
bi_coords, bi_ids,
bi_headers, bi_metadata) = emp._process_data([], 'IQR')
self.assertEqual(coord_ids, ['PC.636', 'PC.635', 'PC.356', 'PC.481',
'PC.354', 'PC.593', 'PC.355', 'PC.607', 'PC.634'])
np.testing.assert_array_almost_equal(coords, self.expected_coords)
obs_pct_var = np.array([26.688705, 16.25637, 13.775413, 11.217216,
10.024775])
np.testing.assert_array_almost_equal(pct_var, obs_pct_var)
np.testing.assert_array_almost_equal(ci, [])
self.assertEqual(headers, ['SampleID', 'Treatment', 'DOB',
'Description'])
self.assertEqual(metadata, self.expected_metadata)
self.assertEqual(names, [0, 1, 2, 3, 4])
self.assertEqual(edges, [])
np.testing.assert_array_almost_equal(bi_coords,
self.expected_biplot_coords)
self.assertEqual(bi_ids,
['f.PC.636', 'f.PC.635', 'f.PC.356', 'f.PC.481',
'f.PC.354'])
self.assertEqual(bi_headers, ['id', 'all'])
self.assertEqual(bi_metadata, [['f.PC.636', 'All elements'],
['f.PC.635', 'All elements'],
['f.PC.356', 'All elements'],
['f.PC.481', 'All elements'],
['f.PC.354', 'All elements']])
def test_process_data_custom_axes(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
(coord_ids, coords, pct_var, ci, headers, metadata, names,
edges,
bi_coords, bi_ids,
bi_headers, bi_metadata) = emp._process_data(['DOB'], 'IQR')
self.assertEqual(coord_ids, ['PC.636', 'PC.635', 'PC.356', 'PC.481',
'PC.354', 'PC.593', 'PC.355', 'PC.607', 'PC.634'])
obs_coords = [[1.322178487895014, -0.651995810831719,
-0.3417784983371589, 0.15713116241738878,
-0.15964022322388774, 0.41511600449567154],
[1.322178487895014, -0.5603276951316744,
0.10857735915373172, -0.32567898978232684,
0.3750137797216106, -0.583487828830988],
[-0.8236274360749414, 0.5394835270542403,
-0.3068324227225251, -0.6770043110217822,
0.203820501907719, 0.1044335488558445],
[0.21458556178898447, 0.09964194790906594,
-0.03293232371368659, 0.14978636968698092,
-0.8160388524355932, -0.301343079001781],
[-0.813231746501206, 0.661089243947507,
-0.014176279685000464, 0.05537095913733857,
-0.11036487613740434, -0.3456924105084198],
[0.3158305385071034, 0.5490376828031979,
0.32957520954888647, 0.7612242145083941,
0.4322721667939822, 0.04825249860931067],
[-0.813231746501206, 0.40202458647314415,
-0.4576554852461752, -0.0728438902229666,
0.04670222577076932, 0.36567512814466946],
[0.30475686917855915, -0.21532604614952783,
1.0, -0.31976501999316115, -0.13561208920603846,
0.35686551552017187],
[1.322178487895014, -0.8236274360749414,
-0.2847775589983077, 0.27177950526966277,
0.16384736680860681, -0.05981937728235736]]
np.testing.assert_array_almost_equal(coords, obs_coords)
obs_pct_var = np.array([-1, 26.688705, 16.25637, 13.775413,
11.217216, 10.024775])
np.testing.assert_array_almost_equal(pct_var, obs_pct_var)
np.testing.assert_array_almost_equal(ci, [])
self.assertEqual(headers, ['SampleID', 'Treatment', 'DOB',
'Description'])
self.assertEqual(metadata, self.expected_metadata)
self.assertEqual(names, ['DOB', 0, 1, 2, 3, 4])
self.assertEqual(edges, [])
self.assertTrue(bi_coords is None)
self.assertTrue(bi_ids is None)
self.assertTrue(bi_headers is None)
self.assertTrue(bi_metadata is None)
def test_custom_axes_missing_headers(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
emp.custom_axes.append(':L')
with self.assertRaises(KeyError):
emp.make_emperor()
def test_custom_axes_no_errors(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
emp.custom_axes.append('DOB')
obs = emp.make_emperor()
self.assertTrue(tcs.CUSTOM_AXES_JSON in obs)
def test_process_jackknifed_data(self):
emp = Emperor(self.ord_res, self.mf, remote=False,
jackknifed=self.jackknifed)
aligned = emp.ordination.samples.index.tolist()
self.assertEqual(emp.jackknifed[0].samples.index.tolist(), aligned)
self.assertEqual(emp.jackknifed[1].samples.index.tolist(), aligned)
self.assertEqual(emp.jackknifed[2].samples.index.tolist(), aligned)
(coord_ids, coords, pct_var, ci, headers, metadata, names,
edges,
bi_coords, bi_ids,
bi_headers, bi_metadata) = emp._process_data([], 'IQR')
self.assertEqual(coord_ids, ['PC.636', 'PC.635', 'PC.356', 'PC.481',
'PC.354', 'PC.593', 'PC.355', 'PC.607', 'PC.634'])
exp_coords = [[-0.7323613329748839, -0.5060247387342096,
-0.2089936328022944, -0.37035261848213485,
0.560102816456614],
[-0.6661577075069334, -0.2217737083659365,
-0.4941091848938413, -0.15063086060307557,
0.09357800544502778],
[-0.10569658584110184, -0.48014086845608406,
-0.7503173511199889, -0.1966206523190892,
0.3288752279579067],
[-0.22411555303555486, -0.27493123505908496,
-0.21093271404078504, -0.8492821018569516,
0.170533519951784],
[-0.07213012997049714, -0.26074072466344955,
-0.23567021423219342, -0.3333389086029676,
0.1585709413204667],
[-0.10306839954771646, -0.16292503176450995,
-0.04434218589935773, -0.13505953366377238,
0.28651010070387867],
[-0.14329582402904856, -0.5913156123027754,
-0.30507284380173166, -0.23792313971010245,
0.5236822252933244],
[-0.4120286058174356, 0.022148368606006386,
-0.48972825402724274, -0.35231914529852637,
0.5171767480000304],
[-0.854640407334614, -0.4637682017836408,
-0.1784746008049904, -0.20721872788742415,
0.2345128716772838]]
np.testing.assert_array_almost_equal(coords, exp_coords)
obs_pct_var = np.array([26.688705, 16.25637, 13.775413,
11.217216, 10.024775])
np.testing.assert_array_almost_equal(pct_var, obs_pct_var)
exp_ci = [[0.1607310442863299, 0.3284924807941013, 0.7369418623398015,
0.4214247905164943, 0.28997362392188486],
[0.21166002475051793, 0.6639877588405441, 0.3368603902230289,
1.0611463515656554, 1.3658809960217244],
[1.302042601434282, 0.34661689146711805, 0.14662608019641343,
0.8068627424977899, 0.44888335820412445],
[0.6505359617817268, 0.4839978226907967, 0.7259215378704654,
0.06648649884271707, 0.9521368980788267],
[1.4777914186973813, 0.4931288899568982, 0.5837728328749483,
0.4459480649311265, 1.017838290883758],
[1.3159259248471549, 0.9939885504306211, 1.6208853472661828,
1.1454098437746723, 0.47651520418913607],
[1.1009478227467375, 0.2673202541132003, 0.46445790715753016,
0.5706778359138301, 0.31601419429730987],
[0.3934051193358155, 1.9557032627879871, 0.3399264680681631,
0.4334141121849759, 0.32062246495971714],
[0.062025942519345234, 0.3579812855706662,
0.9082115096900578, 0.7470141115975886, 0.5904898479721775]]
np.testing.assert_array_almost_equal(ci, exp_ci)
self.assertEqual(headers, ['SampleID', 'Treatment', 'DOB',
'Description'])
self.assertEqual(metadata, self.expected_metadata)
self.assertEqual(names, [0, 1, 2, 3, 4])
self.assertEqual(edges, [])
self.assertTrue(bi_coords is None)
self.assertTrue(bi_ids is None)
self.assertTrue(bi_headers is None)
self.assertTrue(bi_metadata is None)
def test_jackknifed_method_sdev(self):
emp = Emperor(self.ord_res, self.mf, remote=False,
jackknifed=self.jackknifed)
emp.jackknifing_method = 'sdev'
observed = emp._to_dict(emp._process_data(emp.custom_axes,
emp.jackknifing_method))
expected = tcs.JACKKNIFED_SDEV
# the arrays need to be almost equal
obs_coord = observed['plot']['decomposition']['coordinates']
exp_coord = expected['plot']['decomposition']['coordinates']
np.testing.assert_array_almost_equal(obs_coord, exp_coord)
obs_ci = observed['plot']['decomposition']['ci']
exp_ci = expected['plot']['decomposition']['ci']
np.testing.assert_array_almost_equal(obs_ci, exp_ci)
# everything else should be pretty close
for key in ['axes_names', 'edges', 'percents_explained', 'sample_ids']:
self.assertEqual(observed['plot']['decomposition'][key],
expected['plot']['decomposition'][key])
for key in ['metadata_headers', 'settings', 'type']:
self.assertEqual(observed['plot'][key],
expected['plot'][key])
def test_process_procrustes_data(self):
ordinations = self.jackknifed[1:]
emp = Emperor(self.ord_res, self.mf, remote=False,
procrustes=ordinations)
aligned = emp.ordination.samples.index.tolist()
self.assertEqual(emp.jackknifed, [])
self.assertEqual(emp.procrustes[0].samples.index.tolist(), aligned)
self.assertEqual(emp.procrustes[1].samples.index.tolist(), aligned)
(coord_ids, coords, pct_var, ci, headers, metadata, names,
edges,
bi_coords, bi_ids,
bi_headers, bi_metadata) = emp._process_data([], 'IQR')
self.assertEqual(coord_ids,
['PC.636_0', 'PC.635_0', 'PC.356_0', 'PC.481_0',
'PC.354_0', 'PC.593_0', 'PC.355_0', 'PC.607_0',
'PC.634_0',
'PC.636_1', 'PC.635_1', 'PC.356_1', 'PC.481_1',
'PC.354_1', 'PC.593_1', 'PC.355_1', 'PC.607_1',
'PC.634_1',
'PC.636_2', 'PC.635_2', 'PC.356_2', 'PC.481_2',
'PC.354_2', 'PC.593_2', 'PC.355_2', 'PC.607_2',
'PC.634_2'])
np.testing.assert_array_almost_equal(coords, tcs.PROCRUSTES_COORDS)
obs_pct_var = np.array([26.688705, 16.25637, 13.775413,
11.217216, 10.024775])
np.testing.assert_array_almost_equal(pct_var, obs_pct_var)
exp_ci = []
np.testing.assert_array_almost_equal(ci, exp_ci)
self.assertEqual(headers, ['SampleID', 'Treatment', 'DOB',
'Description', '__Procrustes_Names__'])
self.assertEqual(metadata, tcs.PROCRUSTES_MAP)
self.assertEqual(names, [0, 1, 2, 3, 4])
self.assertEqual(edges, [['PC.636_0', 'PC.636_1'],
['PC.635_0', 'PC.635_1'], ['PC.356_0', 'PC.356_1'],
['PC.481_0', 'PC.481_1'], ['PC.354_0', 'PC.354_1'],
['PC.593_0', 'PC.593_1'], ['PC.355_0', 'PC.355_1'],
['PC.607_0', 'PC.607_1'], ['PC.634_0', 'PC.634_1'],
['PC.636_0', 'PC.636_2'], ['PC.635_0', 'PC.635_2'],
['PC.356_0', 'PC.356_2'], ['PC.481_0', 'PC.481_2'],
['PC.354_0', 'PC.354_2'], ['PC.593_0', 'PC.593_2'],
['PC.355_0', 'PC.355_2'], ['PC.607_0', 'PC.607_2'],
['PC.634_0', 'PC.634_2']])
self.assertTrue(bi_coords is None)
self.assertTrue(bi_ids is None)
self.assertTrue(bi_headers is None)
self.assertTrue(bi_metadata is None)
def test_jackknifed_bad_data(self):
with self.assertRaises(TypeError):
Emperor(self.ord_res, self.mf, jackknifed=[1])
with self.assertRaises(TypeError):
Emperor(self.ord_res, self.mf, jackknifed=self.jackknifed + [1])
def test_jackknifed_bad_data_sample_ids(self):
self.jackknifed[0].samples.index = pd.Series(list('abcdefghi'))
with self.assertRaises(ValueError):
Emperor(self.ord_res, self.mf, jackknifed=self.jackknifed)
def test_jackknifed_and_procrustes(self):
a, b, c = self.jackknifed
with self.assertRaises(ValueError):
Emperor(self.ord_res, self.mf, jackknifed=[a, b],
procrustes=[c])
class EmperorSettingsTests(TestCase):
"""Extensively test the settings property and methods"""
def setUp(self):
or_f = StringIO(tcs.PCOA_STRING)
self.ord_res = OrdinationResults.read(or_f)
data = \
[['PC.354', 'Control', '20061218', 'Ctrol_mouse_I.D._354'],
['PC.355', 'Control', '20061218', 'Control_mouse_I.D._355'],
['PC.356', 'Control', '20061126', 'Control_mouse_I.D._356'],
['PC.481', 'Control', '20070314', 'Control_mouse_I.D._481'],
['PC.593', 'Control', '20071210', 'Control_mouse_I.D._593'],
['PC.607', 'Fast', '20071112', 'Fasting_mouse_I.D._607'],
['PC.634', 'Fast', '20080116', 'Fasting_mouse_I.D._634'],
['PC.635', 'Fast', '20080116', 'Fasting_mouse_I.D._635'],
['PC.636', 'Fast', '20080116', 'Fasting_mouse_I.D._636']]
headers = ['SampleID', 'Treatment', 'DOB', 'Description']
self.mf = pd.DataFrame(data=data, columns=headers)
self.mf.set_index('SampleID', inplace=True)
def test_base_data_checks(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
data = {'20061126': '#ff00ff', '20061218': '#ff0000',
'20070314': '#00000f', '20071112': '#ee00ee',
'20071210': '#0000fa', '20080116': '#dedede'}
obs = emp._base_data_checks('DOB', data, str)
self.assertEqual(obs, data)
def test_base_data_checks_with_data_series(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
exp = {'20061126': '#ff00ff', '20061218': '#ff0000',
'20070314': '#00000f', '20071112': '#ee00ee',
'20071210': '#0000fa', '20080116': '#dedede'}
data = pd.Series(exp)
obs = emp._base_data_checks('DOB', data, str)
self.assertEqual(obs, exp)
def test_base_data_checks_with_no_data(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
obs = emp._base_data_checks('DOB', {}, str)
self.assertEqual(obs, {})
obs = emp._base_data_checks('DOB', pd.Series(), str)
self.assertEqual(obs, {})
def test_base_data_checks_category_with_invalid_more_data(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
data = {'20061126': '#ff00ff', '20061218': '#ff0000',
'20070314': '#00000f', '20071112': '#ee00ee',
'20071210': '#0000fa', '20080116': '#dedede', 'foo': '#ff00fb'}
with self.assertRaises(ValueError):
emp._base_data_checks('DOB', data, str)
def test_base_data_checks_category_with_invalid_less_data(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
data = {'20061126': '#ff00ff', '20061218': '#ff0000',
'20070314': '#00000f', '20071112': '#ee00ee',
'20071210': '#0000fa', '20080116': '#dedede'}
del data['20071210']
with self.assertRaises(ValueError):
emp._base_data_checks('DOB', data, str)
def test_base_data_checks_category_does_not_exist(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
with self.assertRaises(KeyError):
emp._base_data_checks('Boaty McBoatFace', None, str)
def test_base_data_checks_category_not_str(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
with self.assertRaises(TypeError):
emp._base_data_checks([], None, str)
with self.assertRaises(TypeError):
emp._base_data_checks(11, None, str)
def test_color_by_category(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
obs = emp.color_by('DOB')
exp = {'color': {"category": 'DOB',
"colormap": 'discrete-coloring-qiime',
"continuous": False,
"data": {}
}
}
self.assertEqual(emp.settings['color'], exp['color'])
self.assertEqual(obs.settings['color'], exp['color'])
def test_color_by_category_and_colormap(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
obs = emp.color_by('DOB', colormap='Dark2')
exp = {'color': {"category": 'DOB',
"colormap": 'Dark2',
"continuous": False,
"data": {}
}
}
self.assertEqual(emp.settings['color'], exp['color'])
self.assertEqual(obs.settings['color'], exp['color'])
def test_color_by_category_continuous(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
obs = emp.color_by('Treatment', colormap='Dark2', continuous=True)
exp = {'color': {"category": 'Treatment',
"colormap": 'Dark2',
"continuous": True,
"data": {}
}
}
self.assertEqual(emp.settings['color'], exp['color'])
self.assertEqual(obs.settings['color'], exp['color'])
def test_color_by_category_with_data(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
data = {'20061126': '#ff00ff', '20061218': '#ff0000',
'20070314': '#00000f', '20071112': '#ee00ee',
'20071210': '#0000fa', '20080116': '#dedede'}
obs = emp.color_by('Treatment', colors=data, colormap='Dark2',
continuous=True)
exp = {'color': {"category": 'Treatment',
"colormap": 'Dark2',
"continuous": True,
"data": {'20061126': '#ff00ff',
'20061218': '#ff0000',
'20070314': '#00000f',
'20071112': '#ee00ee',
'20071210': '#0000fa',
'20080116': '#dedede'
}
}
}
self.assertEqual(emp.settings['color'], exp['color'])
self.assertEqual(obs.settings['color'], exp['color'])
def test_color_by_colormap_not_str(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
with self.assertRaises(TypeError):
emp.color_by('DOB', colormap=11)
with self.assertRaises(TypeError):
emp.color_by('DOB', colormap=[])
with self.assertRaises(TypeError):
emp.color_by('DOB', colormap=(1, 2))
def test_shape_by(self):
emp = Emperor(self.ord_res, self.mf, remote=False)
obs = emp.shape_by('DOB')
exp = {'shape': {"category": 'DOB',
"data": {}
}
}
self.assertEqual(emp.settings['shape'], exp['shape'])
self.assertEqual(obs.settings['shape'], exp['shape'])
obs = emp.shape_by('Treatment')
exp = {'shape': {"category": 'Treatment',
"data": {}
}