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fix for incorrect stats computation in diff exp t-test (#2318)

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* 2211 fixes

* lint

* lint

* add missing test and bug found by test

* change terminology for count distribution

* update scanpy requirement

* update scanpy requirement
This commit is contained in:
Bruce Martin
2021-07-23 11:36:26 -07:00
committed by GitHub
parent 1ebde2213d
commit 1ea2b7fe80
28 changed files with 336 additions and 90 deletions
Download Patch File Download Diff File Expand all files Collapse all files
backend/test/test_czi_hosted/unit/common/config/__init__.py
+3
View File
@@ -131,6 +131,7 @@ class ConfigTests(BaseTest):
environment=None,
aws_secrets_manager_region=None,
aws_secrets_manager_secrets=[],
X_approx_distribution="normal",
config_file_name="app_config.yml",
):
random_num = random.randrange(999999)
@@ -194,6 +195,7 @@ class ConfigTests(BaseTest):
enable_difexp=enable_difexp,
lfc_cutoff=lfc_cutoff,
top_n=top_n,
X_approx_distribution=X_approx_distribution,
config_file_name=f"temp_dataset_config_{random_num}.yml",
)
external_config = self.custom_external_config(
@@ -229,6 +231,7 @@ class ConfigTests(BaseTest):
enable_difexp="true",
lfc_cutoff=0.01,
top_n=10,
X_approx_distribution="normal",
config_file_name="dataset_config.yml",
):
configfile = os.path.join(self.tmp_fixtures_directory, config_file_name)
backend/test/test_czi_hosted/unit/common/config/test_dataset_config.py
+1 -1
View File
@@ -49,7 +49,7 @@ class TestDatasetConfig(ConfigTests):
def test_complete_config_checks_all_attr(self, mock_check_attrs):
mock_check_attrs.side_effect = BaseConfig.validate_correct_type_of_configuration_attribute()
self.dataset_config.complete_config(self.context)
self.assertEqual(mock_check_attrs.call_count, 18)
self.assertEqual(mock_check_attrs.call_count, 19)
def test_app_sets_script_vars(self):
config = self.get_config(scripts=["path/to/script"])
backend/test/test_czi_hosted/unit/compute/test_diffexp_cxg.py
+21 -20
View File
@@ -20,6 +20,7 @@ class DiffExpTest(unittest.TestCase):
adaptor types and different algorithms."""
def load_dataset(self, path, extra_server_config={}, extra_dataset_config={}):
extra_dataset_config["X_approx_distribution"] = "normal" # hardwired for now
config = app_config(path, extra_server_config=extra_server_config, extra_dataset_config=extra_dataset_config)
loader = MatrixDataLoader(path)
adaptor = loader.open(config)
@@ -46,28 +47,28 @@ class DiffExpTest(unittest.TestCase):
"""Checks the results for a specific set of rows selections"""
positive_expects = [
[1712, -0.5525154, 0.0051788902660723345, 1.0],
[1575, 1.0317602, 0.007830310753043345, 1.0],
[693, 0.4703904, 0.008715846769131548, 1.0],
[916, 0.9567287, 0.009080596532247588, 1.0],
[77, 0.02665649, 0.010070392939027756, 1.0],
[782, -1.0981874, 0.010161745218916036, 1.0],
[913, 0.5683986, 0.010782030711612685, 1.0],
[910, 0.83164597, 0.014596411069229197, 1.0],
[1727, 0.4127781, 0.015168372104237176, 1.0],
[1443, -0.8241895, 0.015337080567465522, 1.0]
[1712, 0.24104056, 0.0051788902660723345, 1.0],
[1575, 0.2615018, 0.007830310753043345, 1.0],
[693, 0.23106655, 0.008715846769131548, 1.0],
[916, 0.2395215, 0.009080596532247588, 1.0],
[77, 0.22927025, 0.010070392939027756, 1.0],
[782, 0.20581803, 0.010161745218916036, 1.0],
[913, 0.23841085, 0.010782030711612685, 1.0],
[910, 0.21493295, 0.014596411069229197, 1.0],
[1727, 0.21911663, 0.015168372104237176, 1.0],
[1443, 0.19814226, 0.015337080567465522, 1.0],
]
negative_expects = [
[956, 0.016060986, 0.0008649321884808977, 1.0],
[1124, 0.96602094, 0.0011717216548271284, 1.0],
[1809, 1.1110606, 0.0019304405196777848, 1.0],
[1754, 0.5201581, 0.005691734062127954, 1.0],
[948, 1.6390722, 0.006622111055981219, 1.0],
[1810, 0.78618884, 0.007055917428377063, 1.0],
[779, 1.5241305, 0.007202934422407284, 1.0],
[576, 0.97873515, 0.008272092578813124, 1.0],
[538, 0.89114505, 0.01062259019889307, 1.0],
[436, 0.3119122, 0.01127515110543434, 1.0]
[956, -0.29662406, 0.0008649321884808977, 1.0],
[1124, -0.2607333, 0.0011717216548271284, 1.0],
[1809, -0.24854594, 0.0019304405196777848, 1.0],
[1754, -0.24683577, 0.005691734062127954, 1.0],
[948, -0.18708363, 0.006622111055981219, 1.0],
[1810, -0.2172082, 0.007055917428377063, 1.0],
[779, -0.21150622, 0.007202934422407284, 1.0],
[576, -0.19008157, 0.008272092578813124, 1.0],
[538, -0.21803819, 0.01062259019889307, 1.0],
[436, -0.2100364, 0.01127515110543434, 1.0],
]
self.compare_diffexp_results(results['positive'], positive_expects)