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| author | Frederick Muriuki Muriithi | 2021-09-15 12:08:56 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2021-09-15 12:08:56 +0300 |
| commit | 11632a565a6f901eca852a5a40a6f9fd3170152a (patch) | |
| tree | 6fc57c7b09e2520f438d9842eee70bec67626da2 /tests | |
| parent | b1eb0451578c53afabe4f2054ce08665dec4bb82 (diff) | |
| download | genenetwork3-11632a565a6f901eca852a5a40a6f9fd3170152a.tar.gz | |
Process data into format usable by heatmaps
* gn3/heatmaps.py: implement `process_traits_data_for_heatmap` function, that will process the data into a form usable by heatmaps. * tests/unit/test_heatmaps.py: check that the function processes the data into the correct form.
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/test_heatmaps.py | 107 |
1 files changed, 106 insertions, 1 deletions
diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py index cfdde1e..f3a81c5 100644 --- a/tests/unit/test_heatmaps.py +++ b/tests/unit/test_heatmaps.py @@ -5,7 +5,8 @@ from gn3.heatmaps import ( get_lrs_from_chr, export_trait_data, compute_traits_order, - retrieve_strains_and_values) + retrieve_strains_and_values, + process_traits_data_for_heatmap) strainlist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] trait_data = { @@ -199,3 +200,107 @@ class TestHeatmap(TestCase): [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): + 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]]]) |