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authorBonfaceKilz2021-09-27 13:59:17 +0300
committerGitHub2021-09-27 13:59:17 +0300
commit0cbb6ecde0315b7d6f021cb17406f5e5197e8a05 (patch)
tree0647dddf8b1aa4530476807bfa3a5dfd54a8119f /tests/unit/test_heatmaps.py
parent2cf220a11936125f059dc9b6a494d0f70eac068d (diff)
parenta9fc9814760d205674904f8feb700eadae480fb1 (diff)
downloadgenenetwork3-0cbb6ecde0315b7d6f021cb17406f5e5197e8a05.tar.gz
Merge pull request #37 from genenetwork/heatmap_generation
Heatmap generation
Diffstat (limited to 'tests/unit/test_heatmaps.py')
-rw-r--r--tests/unit/test_heatmaps.py216
1 files changed, 216 insertions, 0 deletions
diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py
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+++ b/tests/unit/test_heatmaps.py
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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_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"]
+trait_data = {
+ "mysqlid": 36688172,
+ "data": {
+ "B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
+ "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
+ "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
+ "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
+ "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
+ "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
+ "BXD21": {"sample_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
+ "BXD24": {"sample_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
+ "BXD27": {"sample_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
+ "BXD28": {"sample_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
+ "BXD32": {"sample_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
+ "BXD39": {"sample_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
+ "BXD40": {"sample_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
+ "BXD42": {"sample_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
+ "BXD6": {"sample_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
+ "BXH14": {"sample_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
+ "BXH19": {"sample_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
+ "BXH2": {"sample_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
+ "BXH22": {"sample_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
+ "BXH4": {"sample_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
+ "BXH6": {"sample_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
+ "BXH7": {"sample_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
+ "BXH8": {"sample_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
+ "BXH9": {"sample_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
+ "C3H/HeJ": {"sample_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
+ "C57BL/6J": {"sample_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
+ "DBA/2J": {"sample_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, samplelist, 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, samplelist, 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_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)
+
+ 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(
+ {**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]]])