From 4a55971a9be54b399c45a53e211df3348df1c52b Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 28 Sep 2021 10:15:43 +0300
Subject: Retrieve loci names ordered by chromosomes
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* gn3/heatmaps.py: implement function
* tests/unit/test_heatmaps.py: add test
Add a function to retrieve the loci names from the traits, ordered by
chromosomes, in alphabetical order.
This is useful to provide the user with more information on hovering over
the heatmap cells: each cell will now display the locus name, trait name and
value associated with it.
---
tests/unit/test_heatmaps.py | 15 +++++++++++++++
1 file changed, 15 insertions(+)
(limited to 'tests/unit')
diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py
index b54e2f3..7b66688 100644
--- a/tests/unit/test_heatmaps.py
+++ b/tests/unit/test_heatmaps.py
@@ -2,6 +2,7 @@
from unittest import TestCase
from gn3.heatmaps import (
cluster_traits,
+ get_loci_names,
get_lrs_from_chr,
export_trait_data,
compute_traits_order,
@@ -214,3 +215,17 @@ class TestHeatmap(TestCase):
[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]]])
+
+ def test_get_loci_names(self):
+ """Check that loci names are retrieved correctly."""
+ for organised, expected in (
+ (organised_trait_1,
+ (("rs258367496", "rs30658298", "rs31443144", "rs32285189",
+ "rs32430919", "rs36251697", "rs6269442"),
+ ("rs31879829", "rs36742481", "rs51852623"))),
+ ({**organised_trait_1, **organised_trait_2},
+ (("rs258367496", "rs30658298", "rs31443144", "rs32285189",
+ "rs32430919", "rs36251697", "rs6269442"),
+ ("rs31879829", "rs36742481", "rs51852623")))):
+ with self.subTest(organised=organised):
+ self.assertEqual(get_loci_names(organised, (1, 2)), expected)
--
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