本文整理汇总了Python中skbio.stats.ordination.PCoA类的典型用法代码示例。如果您正苦于以下问题：Python PCoA类的具体用法？Python PCoA怎么用？Python PCoA使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了PCoA类的10个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: pcoa
def pcoa(lines):
"""Run PCoA on the distance matrix present on lines"""
# Parse the distance matrix
dist_mtx = DistanceMatrix.read(lines)
# Create the PCoA object
pcoa_obj = PCoA(dist_mtx)
# Get the PCoA results and return them
return pcoa_obj.scores()示例2: dm_to_pcoa
def dm_to_pcoa(dm, sample_md, category):
title = "Samples colored by %s." % category
pcoa_results = PCoA(dm).scores()
_ = pcoa_results.plot(df=sample_md,
column=category,
axis_labels=['PC 1', 'PC 2', 'PC 3'],
title=title,
s=35)示例3: test_values
def test_values(self):
"""Adapted from cogent's `test_principal_coordinate_analysis`:
"I took the example in the book (see intro info), and did the
principal coordinates analysis, plotted the data and it looked
right"."""
with warnings.catch_warnings():
warnings.filterwarnings("ignore", category=RuntimeWarning)
ordination = PCoA(self.dist_matrix)
scores = ordination.scores()
exp_eigvals = np.array(
[
0.73599103,
0.26260032,
0.14926222,
0.06990457,
0.02956972,
0.01931184,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
]
)
exp_site = np.loadtxt(get_data_path("exp_PCoAzeros_site"))
exp_prop_expl = np.array(
[
0.58105792,
0.20732046,
0.1178411,
0.05518899,
0.02334502,
0.01524651,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
0.0,
]
)
exp_site_ids = ["0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13"]
# Note the absolute value because column can have signs swapped
npt.assert_almost_equal(scores.eigvals, exp_eigvals)
npt.assert_almost_equal(np.abs(scores.site), exp_site)
npt.assert_almost_equal(scores.proportion_explained, exp_prop_expl)
npt.assert_equal(scores.site_ids, exp_site_ids)示例4: TestPCoAEigenResults
class TestPCoAEigenResults(object):
def setup(self):
dist_matrix = DistanceMatrix.read(get_data_path('PCoA_sample_data_3'))
self.ordination = PCoA(dist_matrix)
self.ids = ['PC.636', 'PC.635', 'PC.356', 'PC.481', 'PC.354', 'PC.593',
'PC.355', 'PC.607', 'PC.634']
def test_values(self):
results = self.ordination.scores()
npt.assert_almost_equal(len(results.eigvals), len(results.site[0]))
expected = np.loadtxt(get_data_path('exp_PCoAEigenResults_site'))
npt.assert_almost_equal(*normalize_signs(expected, results.site))
expected = np.array([0.51236726, 0.30071909, 0.26791207, 0.20898868,
0.19169895, 0.16054235, 0.15017696, 0.12245775,
0.0])
npt.assert_almost_equal(results.eigvals, expected)
expected = np.array([0.2675738328, 0.157044696, 0.1399118638,
0.1091402725, 0.1001110485, 0.0838401162,
0.0784269939, 0.0639511764, 0.0])
npt.assert_almost_equal(results.proportion_explained, expected)
npt.assert_equal(results.site_ids, self.ids)示例5: TestPCoAResultsExtensive
class TestPCoAResultsExtensive(object):
def setup(self):
matrix = np.loadtxt(get_data_path('PCoA_sample_data_2'))
self.ids = [str(i) for i in range(matrix.shape[0])]
dist_matrix = DistanceMatrix(matrix, self.ids)
self.ordination = PCoA(dist_matrix)
def test_values(self):
results = self.ordination.scores()
npt.assert_equal(len(results.eigvals), len(results.site[0]))
expected = np.array([[-0.028597, 0.22903853, 0.07055272,
0.26163576, 0.28398669, 0.0],
[0.37494056, 0.22334055, -0.20892914,
0.05057395, -0.18710366, 0.0],
[-0.33517593, -0.23855979, -0.3099887,
0.11521787, -0.05021553, 0.0],
[0.25412394, -0.4123464, 0.23343642,
0.06403168, -0.00482608, 0.0],
[-0.28256844, 0.18606911, 0.28875631,
-0.06455635, -0.21141632, 0.0],
[0.01727687, 0.012458, -0.07382761,
-0.42690292, 0.1695749, 0.0]])
npt.assert_almost_equal(*normalize_signs(expected, results.site))
expected = np.array([0.3984635, 0.36405689, 0.28804535, 0.27479983,
0.19165361, 0.0])
npt.assert_almost_equal(results.eigvals, expected)
expected = np.array([0.2626621381, 0.2399817314, 0.1898758748,
0.1811445992, 0.1263356565, 0.0])
npt.assert_almost_equal(results.proportion_explained, expected)
npt.assert_equal(results.site_ids, self.ids)示例6: setup
def setup(self):
with open(get_data_path('PCoA_sample_data_3'), 'U') as lines:
dist_matrix = DistanceMatrix.from_file(lines)
self.ordination = PCoA(dist_matrix)
self.ids = ['PC.636', 'PC.635', 'PC.356', 'PC.481', 'PC.354', 'PC.593',
'PC.355', 'PC.607', 'PC.634']示例7: test_F_matrix
def test_F_matrix(self):
F = PCoA._F_matrix(self.matrix2)
expected_F = np.zeros((3, 3))
# Note that `test_make_F_matrix` in cogent is wrong
npt.assert_almost_equal(F, expected_F)示例8: test_E_matrix
def test_E_matrix(self):
E = PCoA._E_matrix(self.matrix)
expected_E = np.array([[-0.5, -2., -4.5],
[-8., -12.5, -18.]])
npt.assert_almost_equal(E, expected_E)示例9: setup
def setup(self):
dist_matrix = DistanceMatrix.read(get_data_path('PCoA_sample_data_3'))
self.ordination = PCoA(dist_matrix)
self.ids = ['PC.636', 'PC.635', 'PC.356', 'PC.481', 'PC.354', 'PC.593',
'PC.355', 'PC.607', 'PC.634']示例10: setup
def setup(self):
dist_matrix = DistanceMatrix.read(get_data_path("PCoA_sample_data_3"))
self.ordination = PCoA(dist_matrix)
self.ids = ["PC.636", "PC.635", "PC.356", "PC.481", "PC.354", "PC.593", "PC.355", "PC.607", "PC.634"]