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"""Module contains tests for gn3.heatmaps.heatmaps"""
from unittest import TestCase
from gn3.heatmaps import (
cluster_traits,
get_lrs_from_chr,
export_trait_data,
compute_traits_order,
retrieve_strains_and_values,
process_traits_data_for_heatmap)
strainlist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
trait_data = {
"mysqlid": 36688172,
"data": {
"B6cC3-1": {"strain_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
"BXD1": {"strain_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
"BXD12": {"strain_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
"BXD16": {"strain_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
"BXD19": {"strain_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
"BXD2": {"strain_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
"BXD21": {"strain_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
"BXD24": {"strain_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
"BXD27": {"strain_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
"BXD28": {"strain_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
"BXD32": {"strain_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
"BXD39": {"strain_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
"BXD40": {"strain_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
"BXD42": {"strain_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
"BXD6": {"strain_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
"BXH14": {"strain_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
"BXH19": {"strain_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
"BXH2": {"strain_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
"BXH22": {"strain_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
"BXH4": {"strain_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
"BXH6": {"strain_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
"BXH7": {"strain_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
"BXH8": {"strain_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
"BXH9": {"strain_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
"C3H/HeJ": {"strain_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
"C57BL/6J": {"strain_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
"DBA/2J": {"strain_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
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"""
def test_export_trait_data_dtype(self):
"""
Test `export_trait_data` with different values for the `dtype` keyword
argument
"""
for dtype, expected in [
["val", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["var", (None, None, None, None, None, None)],
["N", (None, None, None, None, None, None)],
["all", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)]]:
with self.subTest(dtype=dtype):
self.assertEqual(
export_trait_data(trait_data, strainlist, dtype=dtype),
expected)
def test_export_trait_data_dtype_all_flags(self):
"""
Test `export_trait_data` with different values for the `dtype` keyword
argument and the different flags set up
"""
for dtype, vflag, nflag, expected in [
["val", False, False,
(7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["val", False, True,
(7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["val", True, False,
(7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["val", True, True,
(7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["var", False, False, (None, None, None, None, None, None)],
["var", False, True, (None, None, None, None, None, None)],
["var", True, False, (None, None, None, None, None, None)],
["var", True, True, (None, None, None, None, None, None)],
["N", False, False, (None, None, None, None, None, None)],
["N", False, True, (None, None, None, None, None, None)],
["N", True, False, (None, None, None, None, None, None)],
["N", True, True, (None, None, None, None, None, None)],
["all", False, False,
(7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)],
["all", False, True,
(7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
8.30401, None, 7.80944, None)],
["all", True, False,
(7.51879, None, 7.77141, None, 8.39265, None, 8.17443, None,
8.30401, None, 7.80944, None)],
["all", True, True,
(7.51879, None, None, 7.77141, None, None, 8.39265, None, None,
8.17443, None, None, 8.30401, None, None, 7.80944, None, None)]
]:
with self.subTest(dtype=dtype, vflag=vflag, nflag=nflag):
self.assertEqual(
export_trait_data(
trait_data, strainlist, dtype=dtype, var_exists=vflag,
n_exists=nflag),
expected)
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)]
self.assertEqual(
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)))
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))
def test_retrieve_strains_and_values(self):
"""Test retrieval of strains 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(strainlist=slist, traitdata=tdata):
self.assertEqual(
retrieve_strains_and_values(orders, slist, tdata), expected)
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)
def test_process_traits_data_for_heatmap(self):
"""Check for correct processing of data for heatmap generation."""
self.assertEqual(
process_traits_data_for_heatmap(
{"1": {
"ID": "T1",
"chromosomes": {
1: {"Chr": 1,
"loci": [
{
"Locus": "rs31443144", "cM": 1.500, "Mb": 3.010,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs6269442", "cM": 1.500, "Mb": 3.492,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs32285189", "cM": 1.630, "Mb": 3.511,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs258367496", "cM": 1.630, "Mb": 3.660,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs32430919", "cM": 1.750, "Mb": 3.777,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs36251697", "cM": 1.880, "Mb": 3.812,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs30658298", "cM": 2.010, "Mb": 4.431,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
}]},
2: {"Chr": 2,
"loci": [
{
"Locus": "rs51852623", "cM": 2.010, "Mb": 4.447,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs31879829", "cM": 2.140, "Mb": 4.519,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs36742481", "cM": 2.140, "Mb": 4.776,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
}]}}},
"2": {
"ID": "T1",
"chromosomes": {
1: {"Chr": 1,
"loci": [
{
"Locus": "rs31443144", "cM": 1.500, "Mb": 3.010,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs6269442", "cM": 1.500, "Mb": 3.492,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs32285189", "cM": 1.630, "Mb": 3.511,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs258367496", "cM": 1.630, "Mb": 3.660,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs32430919", "cM": 1.750, "Mb": 3.777,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs36251697", "cM": 1.880, "Mb": 3.812,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs30658298", "cM": 2.010, "Mb": 4.431,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
}]},
2: {"Chr": 2,
"loci": [
{
"Locus": "rs51852623", "cM": 2.010, "Mb": 4.447,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs31879829", "cM": 2.140, "Mb": 4.519,
"LRS": 0.500, "Additive": -0.074, "pValue": 1.000
},
{
"Locus": "rs36742481", "cM": 2.140, "Mb": 4.776,
"LRS": 0.579, "Additive": -0.074, "pValue": 1.000
}]}}}},
["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]]])
|
