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.
---
 gn3/heatmaps.py             | 28 +++++++++++++++++++++++++++-
 tests/unit/test_heatmaps.py | 15 +++++++++++++++
 2 files changed, 42 insertions(+), 1 deletion(-)

diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py
index 2ef2d16..9c10ba3 100644
--- a/gn3/heatmaps.py
+++ b/gn3/heatmaps.py
@@ -4,7 +4,7 @@ generate various kinds of heatmaps.
 """
 
 from functools import reduce
-from typing import Any, Dict, Sequence
+from typing import Any, Dict, Union, Sequence
 
 import numpy as np
 import plotly.graph_objects as go # type: ignore
@@ -142,6 +142,32 @@ def cluster_traits(traits_data_list: Sequence[Dict]):
 
     return tuple(__cluster(tdata_i) for tdata_i in enumerate(traits_data_list))
 
+def get_loci_names(
+        organised: dict,
+        chromosome_names: Sequence[str]) -> Sequence[Sequence[str]]:
+    """
+    Get the loci names organised by the same order as the `chromosome_names`.
+    """
+    def __get_trait_loci(accumulator, trait):
+        chrs = tuple(trait["chromosomes"].keys())
+        trait_loci = {
+            _chr: tuple(
+                locus["Locus"]
+                for locus in trait["chromosomes"][_chr]["loci"]
+            ) for _chr in chrs
+        }
+        return {
+            **accumulator,
+            **{
+                _chr: tuple(sorted(set(
+                    trait_loci[_chr] + accumulator.get(_chr, tuple()))))
+                for _chr in trait_loci.keys()
+            }
+        }
+    loci_dict: Dict[Union[str, int], Sequence[str]] = reduce(
+        __get_trait_loci, [v[1] for v in organised.items()], {})
+    return tuple(loci_dict[_chr] for _chr in chromosome_names)
+
 def build_heatmap(traits_names, conn: Any):
     """
     heatmap function
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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