diff options
| -rw-r--r-- | gn3/computations/heatmap.py | 51 | ||||
| -rw-r--r-- | tests/unit/computations/test_heatmap.py | 37 |
2 files changed, 85 insertions, 3 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py index 3c35029..c9c2b8a 100644 --- a/gn3/computations/heatmap.py +++ b/gn3/computations/heatmap.py @@ -156,8 +156,8 @@ def heatmap_data(formd, search_result, conn: Any): traits_details = [ __retrieve_traitlist_and_datalist(threshold, fullname) for fullname in search_result] - traits_list = map(lambda x: x[0], traits_details) - traits_data_list = map(lambda x: x[1], traits_details) + traits_list = tuple(x[0] for x in traits_details) + traits_data_list = tuple(x[1] for x in traits_details) return { "target_description_checked": formd.formdata.getvalue( @@ -175,3 +175,50 @@ def heatmap_data(formd, search_result, conn: Any): "traits_list": traits_list, "traits_data_list": traits_data_list } + +def compute_heatmap_order( + slink_data, xoffset: int = 40, neworder: tuple = tuple()): + """ + Compute the data used for drawing the heatmap proper 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): + print("norder:{}, slnk_dt:{}".format(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])) + + if isinstance(slnk_dt[0], int): + return norder + ((xoffset + 20, slnk_dt[0]), ) + + if isinstance(slnk_dt[1], int): + return norder + ((xoffset + d_1[0] + 20, slnk_dt[1]), ) + + return __order_maker(__order_maker(norder, slnk_dt[0]), slnk_dt[1]) + + return __order_maker(neworder, slink_data) + +def retrieve_strains_and_values(strainlist, trait_data): + """ + Get the strains and their corresponding values from `strainlist` and + `trait_data`. + + This migrates the code in + https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L215-221 + """ + def __strains_and_values(acc, i): + if trait_data[i] is None: + return acc + if len(acc) == 0: + return ((strainlist[i], ), (trait_data[i], )) + _strains = acc[0] + _vals = acc[1] + return (_strains + (strainlist[i], ), _vals + (trait_data[i], )) + return reduce( + __strains_and_values, range(len(strainlist)), (tuple(), tuple())) diff --git a/tests/unit/computations/test_heatmap.py b/tests/unit/computations/test_heatmap.py index 650cb45..686288d 100644 --- a/tests/unit/computations/test_heatmap.py +++ b/tests/unit/computations/test_heatmap.py @@ -1,6 +1,10 @@ """Module contains tests for gn3.computations.heatmap""" from unittest import TestCase -from gn3.computations.heatmap import cluster_traits, export_trait_data +from gn3.computations.heatmap import ( + cluster_traits, + export_trait_data, + compute_heatmap_order, + retrieve_strains_and_values) strainlist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] trait_data = { @@ -34,6 +38,16 @@ trait_data = { "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}}} +slinked = ( + (((0, 2, 0.16381088984330505), + ((1, 7, 0.06024619831474998), 5, 0.19179284676938602), + 0.20337048635536847), + 9, + 0.23451785425383564), + ((3, (6, 8, 0.2140799896286565), 0.25879514152086425), + 4, 0.8968250491499363), + 0.9313185954797953) + class TestHeatmap(TestCase): """Class for testing heatmap computation functions""" @@ -141,3 +155,24 @@ class TestHeatmap(TestCase): 0.9313185954797953, 1.1683723389247052, 0.23451785425383564, 1.7413442197913358, 0.33370067057028485, 1.3256191648260216, 0.0))) + + 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) + + def test_retrieve_strains_and_values(self): + """Test retrieval of strains and values.""" + for slist, tdata, expected in [ + [["s1", "s2", "s3", "s4"], [9, None, 5, 4], + (("s1", "s3", "s4"), (9, 5, 4))], + [["s1", "s2", "s3", "s4", "s5"], [6, None, None, 4, None], + (("s1", "s4"), (6, 4))]]: + with self.subTest(strainlist=slist, traitdata=tdata): + self.assertEqual( + retrieve_strains_and_values(slist, tdata), expected) |