def test_integration(self):
"""Integration test of PCoA should work correctly"""
u = array(
[[0., 0.7123611, 0.76849198, 0.80018563, 0.68248524, 0.74634629],
[0.7123611, 0., 0.86645691, 0.80485282, 0.83381301, 0.73881726],
[0.76849198, 0.86645691, 0., 0.82308396, 0.77451746, 0.76498872],
[0.80018563, 0.80485282, 0.82308396, 0., 0.84167365, 0.77614366],
[0.68248524, 0.83381301, 0.77451746, 0.84167365, 0., 0.72661163],
[0.74634629, 0.73881726, 0.76498872, 0.77614366, 0.72661163, 0.]])
e = make_E_matrix(u)
f = make_F_matrix(e)
eigvals, eigvecs = run_eig(f)
bigfirstorder = eigvals.argsort()[::-1]
#eigvecs = eigvecs[bigfirstorder]
#eigvals = eigvals[bigfirstorder]
principal_coords = get_principal_coordinates(eigvals, eigvecs)
principal_coords = principal_coords[bigfirstorder]
expected = array([[
2.85970001e-02, -3.74940557e-01, 3.35175925e-01, -2.54123944e-01,
2.82568441e-01, -1.72768652e-02
],
[
2.29038532e-01, 2.23340550e-01, -2.38559794e-01,
-4.12346397e-01, 1.86069108e-01, 1.24580018e-02
],
[
7.05527166e-02, -2.08929136e-01, -3.09988697e-01,
2.33436419e-01, 2.88756308e-01, -7.38276099e-02
]])
self.assertFloatEqual(abs(principal_coords[[0, 1, 2]]), abs(expected))
def test_integration(self):
"""Integration test of PCoA should work correctly"""
u = array([[ 0. , 0.7123611 , 0.76849198, 0.80018563, 0.68248524, 0.74634629],
[ 0.7123611 , 0. , 0.86645691, 0.80485282, 0.83381301, 0.73881726],
[ 0.76849198, 0.86645691, 0. , 0.82308396, 0.77451746, 0.76498872],
[ 0.80018563, 0.80485282, 0.82308396, 0. , 0.84167365, 0.77614366],
[ 0.68248524, 0.83381301, 0.77451746, 0.84167365, 0. , 0.72661163],
[ 0.74634629, 0.73881726, 0.76498872, 0.77614366, 0.72661163, 0. ]])
e = make_E_matrix(u)
f = make_F_matrix(e)
eigvals, eigvecs = run_eig(f)
bigfirstorder = eigvals.argsort()[::-1]
#eigvecs = eigvecs[bigfirstorder]
#eigvals = eigvals[bigfirstorder]
principal_coords = get_principal_coordinates(eigvals, eigvecs)
principal_coords = principal_coords[bigfirstorder]
expected = array([
[ 2.85970001e-02, -3.74940557e-01, 3.35175925e-01,
-2.54123944e-01, 2.82568441e-01, -1.72768652e-02],
[ 2.29038532e-01, 2.23340550e-01, -2.38559794e-01,
-4.12346397e-01, 1.86069108e-01, 1.24580018e-02],
[ 7.05527166e-02, -2.08929136e-01, -3.09988697e-01,
2.33436419e-01, 2.88756308e-01, -7.38276099e-02]])
self.assertFloatEqual(abs(principal_coords[[0,1,2]]), abs(expected))
def test_make_E_matrix(self):
"""make_E_matrix converts a distance matrix to an E matrix"""
matrix = self.matrix
E_matrix = make_E_matrix(matrix)
self.assertFloatEqual(E_matrix[0, 0], -0.5)
self.assertFloatEqual(E_matrix[0, 1], -2.0)
self.assertFloatEqual(E_matrix[1, 0], -8.0)
self.assertFloatEqual(E_matrix[1, 2], -18.0)
def test_make_E_matrix(self):
"""make_E_matrix converts a distance matrix to an E matrix"""
matrix = self.matrix
E_matrix = make_E_matrix(matrix)
self.assertFloatEqual(E_matrix[0,0], -0.5)
self.assertFloatEqual(E_matrix[0,1], -2.0)
self.assertFloatEqual(E_matrix[1,0], -8.0)
self.assertFloatEqual(E_matrix[1,2], -18.0)