def setUp(self) -> None:
self.bonferroni = ComparisonsCorrection("bonferroni")
self.bonferroni_manual = ComparisonsCorrection(
partial(multipletests, method="bonferroni"),
name="Bonferroni (manual)",
method_type=0)
def setUp(self) -> None:
self.benjamini_hochberg = ComparisonsCorrection("Benjamini-Hochberg")
self.benjamini_hochberg_006 = ComparisonsCorrection(
"Benjamini-Hochberg", alpha=0.06)
self.benjamini_hochberg_006_man_diff_api = ComparisonsCorrection(
self.my_bh_from_sm,
name="Benjamini-Hochberg (manual)",
method_type=1,
statsmodels_api=False)
def setUp(self) -> None:
self.holm_bonferroni = ComparisonsCorrection("holm")
self.holm_bonferroni_006 = ComparisonsCorrection("holm", alpha=0.06)
self.holm_bonferroni_006_manual = ComparisonsCorrection(
partial(multipletests, method="holm"),
name="Holm-Bonferroni (manual)",
method_type=1,
corr_kwargs={"alpha": 0.06})
self.holm_bonferroni_006_manual_bis = ComparisonsCorrection(
partial(multipletests, method="holm", alpha=0.06),
name="Holm-Bonferroni (manual)",
method_type=1)
def test_signif_with_type1_correction_star_replace(self):
bh = ComparisonsCorrection("BH")
self.annotator.configure(comparisons_correction=bh,
correction_format="replace")
self.annotator.set_pvalues(self.pvalues)
self.assertEqual(["ns", "ns", "ns"],
self.annotator.get_annotations_text())
def test_signif_with_type0_correction_star(self):
bonferroni = ComparisonsCorrection("bonferroni")
self.annotator.configure(comparisons_correction=bonferroni)
self.annotator.set_pvalues(self.pvalues)
self.assertEqual(["ns", "ns", "ns"],
self.annotator.get_annotations_text())
def setUp(self) -> None:
self.benjamini_hochberg = ComparisonsCorrection("Benjamini-Hochberg")
self.stat_result = StatResult("Test X",
"X",
"Stat",
1,
0.02,
alpha=0.05)
self.stat_result.correction_method = self.benjamini_hochberg.name
def test_signif_with_type1_correction_simple(self):
bh = ComparisonsCorrection("BH")
self.annotator.configure(comparisons_correction=bh,
pvalue_format={'text_format': 'simple'})
self.annotator.set_pvalues(self.pvalues)
expected = ["p ≤ 0.05 (ns)", "p ≤ 0.05 (ns)", "p = 0.90"]
self.assertEqual(expected, self.annotator.get_annotations_text())
def test_signif_with_type0_correction_simple(self):
bonferroni = ComparisonsCorrection("bonferroni")
self.annotator.configure(comparisons_correction=bonferroni,
pvalue_format={'text_format': 'simple'})
self.annotator.set_pvalues(self.pvalues)
expected = ["p = 0.09", "p = 0.12", "p = 1.00"]
self.assertEqual(expected, self.annotator.get_annotations_text())
def test_signif_with_type1_correction_star_abnormal_num_comparisons(self):
bh = ComparisonsCorrection("BH")
self.annotator.configure(comparisons_correction=bh)
with self.assertWarnsRegex(UserWarning, "Manually-specified"):
self.annotator.set_pvalues(self.pvalues, num_comparisons=1)
def test_signif_with_type1_correction_star_incorrect_num_comparisons(self):
bh = ComparisonsCorrection("BH")
self.annotator.configure(comparisons_correction=bh)
with self.assertRaisesRegex(ValueError, "positive"):
self.annotator.set_pvalues(self.pvalues, num_comparisons=0)
def test_signif_with_type1_correction_star(self):
bh = ComparisonsCorrection("BH")
self.annotator.configure(comparisons_correction=bh)
self.annotator.set_pvalues(self.pvalues)
self.assertEqual(["* (ns)", "* (ns)", "ns"],
self.annotator.get_annotations_text())
def test_raises_not_implemented(self):
with self.assertRaises(NotImplementedError):
ComparisonsCorrection('that method')