Test the clustering

Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi

* gn3/computations/heatmap.py: Fix clustering bugs
* tests/unit/computations/test_heatmap.py: Add new tests. Fix linting issues.

  Test and fix the clustering function.

1 files changed, 99 insertions, 10 deletions

diff --git a/tests/unit/computations/test_heatmap.py b/tests/unit/computations/test_heatmap.py
index 78303ae..650cb45 100644
--- a/tests/unit/computations/test_heatmap.py
+++ b/tests/unit/computations/test_heatmap.py
@@ -1,9 +1,38 @@
 """Module contains tests for gn3.computations.heatmap"""
 from unittest import TestCase
-from gn3.computations.heatmap import export_trait_data
+from gn3.computations.heatmap import cluster_traits, export_trait_data
 
 strainlist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"]
-trait_data = {"mysqlid": 36688172, "data": {"B6cC3-1": {"strain_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None}, "BXD1": {"strain_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None}, "BXD12": {"strain_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None}, "BXD16": {"strain_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None}, "BXD19": {"strain_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None}, "BXD2": {"strain_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None}, "BXD21": {"strain_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None}, "BXD24": {"strain_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None}, "BXD27": {"strain_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None}, "BXD28": {"strain_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None}, "BXD32": {"strain_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None}, "BXD39": {"strain_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None}, "BXD40": {"strain_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None}, "BXD42": {"strain_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None}, "BXD6": {"strain_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None}, "BXH14": {"strain_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None}, "BXH19": {"strain_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None}, "BXH2": {"strain_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None}, "BXH22": {"strain_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None}, "BXH4": {"strain_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None}, "BXH6": {"strain_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None}, "BXH7": {"strain_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None}, "BXH8": {"strain_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None}, "BXH9": {"strain_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None}, "C3H/HeJ": {"strain_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None}, "C57BL/6J": {"strain_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None}, "DBA/2J": {"strain_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
+trait_data = {
+    "mysqlid": 36688172,
+    "data": {
+        "B6cC3-1": {"strain_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None},
+        "BXD1": {"strain_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None},
+        "BXD12": {"strain_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None},
+        "BXD16": {"strain_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None},
+        "BXD19": {"strain_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None},
+        "BXD2": {"strain_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None},
+        "BXD21": {"strain_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None},
+        "BXD24": {"strain_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None},
+        "BXD27": {"strain_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None},
+        "BXD28": {"strain_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None},
+        "BXD32": {"strain_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None},
+        "BXD39": {"strain_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None},
+        "BXD40": {"strain_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None},
+        "BXD42": {"strain_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None},
+        "BXD6": {"strain_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None},
+        "BXH14": {"strain_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None},
+        "BXH19": {"strain_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None},
+        "BXH2": {"strain_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None},
+        "BXH22": {"strain_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None},
+        "BXH4": {"strain_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None},
+        "BXH6": {"strain_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None},
+        "BXH7": {"strain_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None},
+        "BXH8": {"strain_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None},
+        "BXH9": {"strain_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None},
+        "C3H/HeJ": {"strain_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None},
+        "C57BL/6J": {"strain_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None},
+        "DBA/2J": {"strain_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}}
 
 class TestHeatmap(TestCase):
     """Class for testing heatmap computation functions"""
@@ -29,10 +58,14 @@ class TestHeatmap(TestCase):
         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)],
+                ["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)],
@@ -41,10 +74,17 @@ class TestHeatmap(TestCase):
                 ["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)]
+                ["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(
@@ -52,3 +92,52 @@ class TestHeatmap(TestCase):
                         trait_data, strainlist, 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)))