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.
---
 gn3/computations/heatmap.py | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

(limited to 'gn3/computations')

diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py
index ccce385..8727c92 100644
--- a/gn3/computations/heatmap.py
+++ b/gn3/computations/heatmap.py
@@ -180,28 +180,24 @@ def heatmap_data(traits_names, conn: Any):
         "traits_filename": traits_filename
     }
 
-def compute_heatmap_order(
-        slink_data, xoffset: int = 40, neworder: tuple = tuple()):
+def compute_traits_order(slink_data, neworder: tuple = tuple()):
     """
-    Compute the data used for drawing the heatmap proper from `slink_data`.
+    Compute the order of the traits for clustering from `slink_data`.
 
     This function tries to reproduce the creation and update of the `neworder`
     variable in
     https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L120
     and in the `web.webqtl.heatmap.Heatmap.draw` function in GN1
     """
-    d_1 = (0, 0, 0) # returned from self.draw in lines 391 and 399. This is just a placeholder
-
     def __order_maker(norder, slnk_dt):
         if isinstance(slnk_dt[0], int) and isinstance(slnk_dt[1], int):
-            return norder + (
-                (xoffset+20, slnk_dt[0]), (xoffset + 40, slnk_dt[1]))
+            return norder + (slnk_dt[0], slnk_dt[1])
 
         if isinstance(slnk_dt[0], int):
-            return norder + ((xoffset + 20, slnk_dt[0]), )
+            return __order_maker((norder + (slnk_dt[0], )), slnk_dt[1])
 
         if isinstance(slnk_dt[1], int):
-            return norder + ((xoffset + d_1[0] + 20, slnk_dt[1]), )
+            return __order_maker(norder, slnk_dt[0]) + (slnk_dt[1], )
 
         return __order_maker(__order_maker(norder, slnk_dt[0]), slnk_dt[1])
 
@@ -222,7 +218,7 @@ def retrieve_strains_and_values(orders, strainlist, traits_data_list):
     values = []
     rets = []
     for order in orders:
-        temp_val = traits_data_list[order[1]]
+        temp_val = traits_data_list[order]
         for i, strain in enumerate(strainlist):
             if temp_val[i] is not None:
                 strains.append(strain)
-- 
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