def test_get_ordered_coordinates(self):
"""get_ordered_coordinates functions as expected """
pc_lines = ["Eigvals\t4",
"191.54\t169.99\t30.45\t19.19",
"",
"Proportion explained\t4",
"18.13\t16.09\t2.88\t1.66",
"",
"Species\t0\t0",
"",
"Site\t5\t4",
"s1\t-0.049\t0.245\t0.146\t-0.036",
"s5\t-0.267\t-0.228\t-0.024\t-0.095",
"s3\t-0.285\t-0.260\t-0.017\t-0.070",
"s2\t-0.002\t0.216\t-0.052\t-0.085",
"s4\t-0.328\t-0.299\t-0.025\t0.051",
"",
"Biplot\t0\t0",
"",
"Site constraints\t0\t0",
""]
pc = parse_coords(StringIO('\n'.join(pc_lines)))
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.002, 0.216, -0.052, -0.085],
[-0.285, -0.260, -0.017, -0.070],
[-0.328, -0.299, -0.025, 0.051],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's2', 's3', 's4', 's5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0], pc[1], ['s1', 's2', 's3', 's4', 's5'])
assert_almost_equal(actual_coords, expected_coords)
self.assertEqual(actual_sids, expected_sids)
pc = parse_coords(StringIO('\n'.join(pc_lines)))
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0], pc[1], ['s1', 's5'])
assert_almost_equal(actual_coords, expected_coords)
self.assertEqual(actual_sids, expected_sids)
pc = parse_coords(StringIO('\n'.join(pc_lines)))
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0], pc[1], ['s1', 's6', 's5'])
assert_almost_equal(actual_coords, expected_coords)
self.assertEqual(actual_sids, expected_sids)
pc = parse_coords(StringIO('\n'.join(pc_lines)))
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's5']
self.assertRaises(ValueError, get_ordered_coordinates,
pc[0], pc[1], ['s1', 's6', 's5'], strict=True)
def test_get_ordered_coordinates(self):
"""get_ordered_coordinates functions as expected """
pc_lines = [
"Eigvals\t4", "191.54\t169.99\t30.45\t19.19", "",
"Proportion explained\t4", "18.13\t16.09\t2.88\t1.66", "",
"Species\t0\t0", "", "Site\t5\t4",
"s1\t-0.049\t0.245\t0.146\t-0.036",
"s5\t-0.267\t-0.228\t-0.024\t-0.095",
"s3\t-0.285\t-0.260\t-0.017\t-0.070",
"s2\t-0.002\t0.216\t-0.052\t-0.085",
"s4\t-0.328\t-0.299\t-0.025\t0.051", "", "Biplot\t0\t0", "",
"Site constraints\t0\t0", ""
]
pc = parse_coords(StringIO('\n'.join(pc_lines)))
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.002, 0.216, -0.052, -0.085],
[-0.285, -0.260, -0.017, -0.070],
[-0.328, -0.299, -0.025, 0.051],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's2', 's3', 's4', 's5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0], pc[1], ['s1', 's2', 's3', 's4', 's5'])
assert_almost_equal(actual_coords, expected_coords)
self.assertEqual(actual_sids, expected_sids)
pc = parse_coords(StringIO('\n'.join(pc_lines)))
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0], pc[1], ['s1', 's5'])
assert_almost_equal(actual_coords, expected_coords)
self.assertEqual(actual_sids, expected_sids)
pc = parse_coords(StringIO('\n'.join(pc_lines)))
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0], pc[1], ['s1', 's6', 's5'])
assert_almost_equal(actual_coords, expected_coords)
self.assertEqual(actual_sids, expected_sids)
pc = parse_coords(StringIO('\n'.join(pc_lines)))
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's5']
self.assertRaises(ValueError,
get_ordered_coordinates,
pc[0],
pc[1], ['s1', 's6', 's5'],
strict=True)
def test_get_ordered_coordinates(self):
"""get_ordered_coordinates functions as expected """
pc_lines = [
"pc vector number\t1\t2\t3\t4", "s1\t-0.049\t0.245\t0.146\t-0.036",
"s5\t-0.267\t-0.228\t-0.024\t-0.095",
"s3\t-0.285\t-0.260\t-0.017\t-0.070",
"s2\t-0.002\t0.216\t-0.052\t-0.085",
"s4\t-0.328\t-0.299\t-0.025\t0.051", "", "",
"eigvals\t191.54\t169.99\t30.45\t19.19",
"% variation explained\t18.13\t16.09\t2.88\t1.66"
]
pc = parse_coords(pc_lines)
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.002, 0.216, -0.052, -0.085],
[-0.285, -0.260, -0.017, -0.070],
[-0.328, -0.299, -0.025, 0.051],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's2', 's3', 's4', 's5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0], pc[1], ['s1', 's2', 's3', 's4', 's5'])
self.assertEqual(actual_coords, expected_coords)
self.assertEqual(actual_sids, expected_sids)
pc = parse_coords(pc_lines)
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0], pc[1], ['s1', 's5'])
self.assertEqual(actual_coords, expected_coords)
self.assertEqual(actual_sids, expected_sids)
pc = parse_coords(pc_lines)
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0], pc[1], ['s1', 's6', 's5'])
self.assertEqual(actual_coords, expected_coords)
self.assertEqual(actual_sids, expected_sids)
pc = parse_coords(pc_lines)
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1', 's5']
self.assertRaises(ValueError,
get_ordered_coordinates,
pc[0],
pc[1], ['s1', 's6', 's5'],
strict=True)
def test_get_ordered_coordinates(self):
"""get_ordered_coordinates functions as expected """
pc_lines = ["pc vector number\t1\t2\t3\t4",
"s1\t-0.049\t0.245\t0.146\t-0.036",
"s5\t-0.267\t-0.228\t-0.024\t-0.095",
"s3\t-0.285\t-0.260\t-0.017\t-0.070",
"s2\t-0.002\t0.216\t-0.052\t-0.085",
"s4\t-0.328\t-0.299\t-0.025\t0.051",
"",
"",
"eigvals\t191.54\t169.99\t30.45\t19.19",
"%% variation explained\t18.13\t16.09\t2.88\t1.66"]
pc = parse_coords(pc_lines)
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.002, 0.216, -0.052, -0.085],
[-0.285, -0.260, -0.017, -0.070],
[-0.328, -0.299, -0.025, 0.051],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1','s2','s3','s4','s5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0],pc[1],['s1','s2','s3','s4','s5'])
self.assertEqual(actual_coords,expected_coords)
self.assertEqual(actual_sids,expected_sids)
pc = parse_coords(pc_lines)
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1','s5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0],pc[1],['s1','s5'])
self.assertEqual(actual_coords,expected_coords)
self.assertEqual(actual_sids,expected_sids)
pc = parse_coords(pc_lines)
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1','s5']
actual_coords, actual_sids = get_ordered_coordinates(
pc[0],pc[1],['s1','s6','s5'])
self.assertEqual(actual_coords,expected_coords)
self.assertEqual(actual_sids,expected_sids)
pc = parse_coords(pc_lines)
expected_coords = [[-0.049, 0.245, 0.146, -0.036],
[-0.267, -0.228, -0.024, -0.095]]
expected_sids = ['s1','s5']
self.assertRaises(ValueError,get_ordered_coordinates,
pc[0],pc[1],['s1','s6','s5'],strict=True)
def ugly_pc_function(m, pc_h, pc, inclusion_fields, disturbed_fields, personal_id, output_fp):
self_pc1s = []
self_pc2s = []
self_pc3s = []
other_pc1s = []
other_pc2s = []
other_pc3s = []
for inclusion_field in inclusion_fields:
timeseries_sample_ids = get_timeseries_sample_ids(
mapping_d=m,
inclusion_field=inclusion_field,
inclusion_value="Yes",
personal_id_field="PersonalID",
disturbed_fields=disturbed_fields,
disturbed_value="Yes",
time_field="WeeksSinceStart",
)
try:
self_sample_ids = [e[1] for e in timeseries_sample_ids[personal_id]]
except KeyError:
self_sample_ids = []
self_coordinates, order = get_ordered_coordinates(pc_h, pc, self_sample_ids)
self_pc1 = []
self_pc2 = []
self_pc3 = []
for vector in self_coordinates:
self_pc1.append(vector[0])
self_pc2.append(vector[1])
self_pc3.append(vector[2])
self_pc1s.append(self_pc1)
self_pc2s.append(self_pc2)
self_pc3s.append(self_pc3)
other_sample_ids = []
for k, v in timeseries_sample_ids.items():
if k != personal_id:
other_sample_ids.extend([e[1] for e in v])
other_coordinates, order = get_ordered_coordinates(pc_h, pc, other_sample_ids)
other_pc1 = []
other_pc2 = []
other_pc3 = []
for vector in other_coordinates:
other_pc1.append(vector[0])
other_pc2.append(vector[1])
other_pc3.append(vector[2])
other_pc1s.append(other_pc1)
other_pc2s.append(other_pc2)
other_pc3s.append(other_pc3)
plot_self_v_other_pcoa(
self_pc1s,
self_pc2s,
self_pc3s,
other_pc1s,
other_pc2s,
other_pc3s,
["r", "r", "r", "r"],
["b", "g", "r", "k"],
["gut", "tongue", "palm", "forehead"],
output_fp,
disturbed_markers=None,
)
