diff options
| -rw-r--r-- | gn3/computations/heatmap.py | 16 | ||||
| -rw-r--r-- | tests/unit/computations/test_heatmap.py | 11 |
2 files changed, 9 insertions, 18 deletions
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) 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.""" |