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| author | Muriithi Frederick Muriuki | 2021-09-08 06:52:01 +0300 |
|---|---|---|
| committer | Muriithi Frederick Muriuki | 2021-09-08 07:02:20 +0300 |
| commit | 31ca02d1f095c2cc667e5b7d49131d702982f321 (patch) | |
| tree | 734f3a379fac6f8648a9228fb6f89f30ea2952b9 /tests | |
| parent | d4943f1d01d89a3928c905f80914a23144126c8e (diff) | |
| download | genenetwork3-31ca02d1f095c2cc667e5b7d49131d702982f321.tar.gz | |
Fix the traits order computations for clustering
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/computations/heatmap.py: Fix ordering function
* tests/unit/computations/test_heatmap.py: update test
The order of the traits is important for the clustering algorithm, since the
clustering seems to use the distance of one trait from another to determine
how to order them.
This commit also gets rid of the xoffset argument that is not important to
the ordering, and was used in the older GN1 to determine how to draw the
clustering lines.
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/unit/computations/test_heatmap.py | 11 |
1 files changed, 3 insertions, 8 deletions
diff --git a/tests/unit/computations/test_heatmap.py b/tests/unit/computations/test_heatmap.py index 87f8e45..f1bbefc 100644 --- a/tests/unit/computations/test_heatmap.py +++ b/tests/unit/computations/test_heatmap.py @@ -3,7 +3,7 @@ from unittest import TestCase from gn3.computations.heatmap import ( cluster_traits, export_trait_data, - compute_heatmap_order, + compute_traits_order, retrieve_strains_and_values) strainlist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] @@ -158,13 +158,8 @@ class TestHeatmap(TestCase): def test_compute_heatmap_order(self): """Test the orders.""" - for xoff, expected in [ - (40, ((60, 9), (60, 4))), - (30, ((50, 9), (50, 4))), - (20, ((40, 9), (40, 4)))]: - with self.subTest(xoffset=xoff): - self.assertEqual( - compute_heatmap_order(slinked, xoffset=xoff), expected) + 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.""" |