1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
|
"""Module contains tests for gn3.heatmaps.heatmaps"""
from unittest import TestCase
import pytest
from numpy.testing import assert_allclose
from gn3.heatmaps import (
cluster_traits,
get_loci_names,
get_lrs_from_chr,
compute_traits_order,
retrieve_samples_and_values,
process_traits_data_for_heatmap)
from tests.unit.sample_test_data import organised_trait_1, organised_trait_2
samplelist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
slinked = (
(((0, 2, 0.16381088984330505),
((1, 7, 0.06024619831474998), 5, 0.19179284676938602),
0.20337048635536847),
9,
0.23451785425383564),
((3, (6, 8, 0.2140799896286565), 0.25879514152086425),
4, 0.8968250491499363),
0.9313185954797953)
class TestHeatmap(TestCase):
"""Class for testing heatmap computation functions"""
@pytest.mark.unit_test
def test_cluster_traits(self):
"""
Test that the clustering is working as expected.
"""
traits_data_list = [
(7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944),
(6.1427, 6.50588, 7.73705, 6.68328, 7.49293, 7.27398),
(8.4211, 8.30581, 9.24076, 8.51173, 9.18455, 8.36077),
(10.0904, 10.6509, 9.36716, 9.91202, 8.57444, 10.5731),
(10.188, 9.76652, 9.54813, 9.05074, 9.52319, 9.10505),
(6.74676, 7.01029, 7.54169, 6.48574, 7.01427, 7.26815),
(6.39359, 6.85321, 5.78337, 7.11141, 6.22101, 6.16544),
(6.84118, 7.08432, 7.59844, 7.08229, 7.26774, 7.24991),
(9.45215, 10.6943, 8.64719, 10.1592, 7.75044, 8.78615),
(7.04737, 6.87185, 7.58586, 6.92456, 6.84243, 7.36913)]
assert_allclose(
cluster_traits(traits_data_list),
((0.0, 0.20337048635536847, 0.16381088984330505, 1.7388553629398245,
1.5025235756329178, 0.6952839500255574, 1.271661230252733,
0.2100487290977544, 1.4699690641062024, 0.7934461515867415),
(0.20337048635536847, 0.0, 0.2198321044997198, 1.5753041735592204,
1.4815755944537086, 0.26087293140686374, 1.6939790104301427,
0.06024619831474998, 1.7430082449189215, 0.4497104244247795),
(0.16381088984330505, 0.2198321044997198, 0.0, 1.9073926868549234,
1.0396738891139845, 0.5278328671176757, 1.6275069061182947,
0.2636503792482082, 1.739617877037615, 0.7127042590637039),
(1.7388553629398245, 1.5753041735592204, 1.9073926868549234, 0.0,
0.9936846292920328, 1.1169999189889366, 0.6007483980555253,
1.430209221053372, 0.25879514152086425, 0.9313185954797953),
(1.5025235756329178, 1.4815755944537086, 1.0396738891139845,
0.9936846292920328, 0.0, 1.027827186339337, 1.1441743109173244,
1.4122477962364253, 0.8968250491499363, 1.1683723389247052),
(0.6952839500255574, 0.26087293140686374, 0.5278328671176757,
1.1169999189889366, 1.027827186339337, 0.0, 1.8420471110023269,
0.19179284676938602, 1.4875072385631605, 0.23451785425383564),
(1.271661230252733, 1.6939790104301427, 1.6275069061182947,
0.6007483980555253, 1.1441743109173244, 1.8420471110023269, 0.0,
1.6540234785929928, 0.2140799896286565, 1.7413442197913358),
(0.2100487290977544, 0.06024619831474998, 0.2636503792482082,
1.430209221053372, 1.4122477962364253, 0.19179284676938602,
1.6540234785929928, 0.0, 1.5225640692832796, 0.33370067057028485),
(1.4699690641062024, 1.7430082449189215, 1.739617877037615,
0.25879514152086425, 0.8968250491499363, 1.4875072385631605,
0.2140799896286565, 1.5225640692832796, 0.0, 1.3256191648260216),
(0.7934461515867415, 0.4497104244247795, 0.7127042590637039,
0.9313185954797953, 1.1683723389247052, 0.23451785425383564,
1.7413442197913358, 0.33370067057028485, 1.3256191648260216,
0.0)))
@pytest.mark.unit_test
def test_compute_heatmap_order(self):
"""Test the orders."""
self.assertEqual(
compute_traits_order(slinked), (0, 2, 1, 7, 5, 9, 3, 6, 8, 4))
@pytest.mark.unit_test
def test_retrieve_samples_and_values(self):
"""Test retrieval of samples and values."""
for orders, slist, tdata, expected in [
[
[2],
["s1", "s2", "s3", "s4"],
[[2, 9, 6, None, 4],
[7, 5, None, None, 4],
[9, None, 5, 4, 7],
[6, None, None, 4, None]],
[[2, ["s1", "s3", "s4"], [9, 5, 4]]]
],
[
[3],
["s1", "s2", "s3", "s4", "s5"],
[[2, 9, 6, None, 4],
[7, 5, None, None, 4],
[9, None, 5, 4, 7],
[6, None, None, 4, None]],
[[3, ["s1", "s4"], [6, 4]]]
]]:
with self.subTest(samplelist=slist, traitdata=tdata):
self.assertEqual(
retrieve_samples_and_values(orders, slist, tdata), expected)
@pytest.mark.unit_test
def test_get_lrs_from_chr(self):
"""Check that function gets correct LRS values"""
for trait, chromosome, expected in [
[{"chromosomes": {}}, 3, [None]],
[{"chromosomes": {3: {"loci": [
{"Locus": "b", "LRS": 1.9},
{"Locus": "a", "LRS": 13.2},
{"Locus": "d", "LRS": 53.21},
{"Locus": "c", "LRS": 2.22}]}}},
3,
[13.2, 1.9, 2.22, 53.21]]]:
with self.subTest(trait=trait, chromosome=chromosome):
self.assertEqual(get_lrs_from_chr(trait, chromosome), expected)
@pytest.mark.unit_test
def test_process_traits_data_for_heatmap(self):
"""Check for correct processing of data for heatmap generation."""
self.assertEqual(
process_traits_data_for_heatmap(
{**organised_trait_1, **organised_trait_2},
["2", "1"],
[1, 2]),
[[[0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]],
[[0.5, 0.579, 0.5],
[0.5, 0.5, 0.5]]])
@pytest.mark.unit_test
def test_get_loci_names(self):
"""Check that loci names are retrieved correctly."""
for organised, expected in (
(organised_trait_1,
(("rs258367496", "rs30658298", "rs31443144", "rs32285189",
"rs32430919", "rs36251697", "rs6269442"),
("rs31879829", "rs36742481", "rs51852623"))),
({**organised_trait_1, **organised_trait_2},
(("rs258367496", "rs30658298", "rs31443144", "rs32285189",
"rs32430919", "rs36251697", "rs6269442"),
("rs31879829", "rs36742481", "rs51852623")))):
with self.subTest(organised=organised):
self.assertEqual(get_loci_names(organised, (1, 2)), expected)
|
