From 31ca02d1f095c2cc667e5b7d49131d702982f321 Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Wed, 8 Sep 2021 06:52:01 +0300 Subject: 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. --- tests/unit/computations/test_heatmap.py | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) (limited to 'tests') 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.""" -- cgit v1.2.3