def _get_results(self,
num_comparisons,
pvalues=None,
**stats_params) -> List[Annotation]:
test_result_list = []
if num_comparisons == "auto":
num_comparisons = len(self._struct_pairs)
for group_struct1, group_struct2 in self._struct_pairs:
group1 = group_struct1['group']
group2 = group_struct2['group']
if self.perform_stat_test:
result = self._get_stat_result_from_test(
group_struct1, group_struct2, num_comparisons,
**stats_params)
else:
result = self._get_custom_results(group_struct1, pvalues)
result.group1 = group1
result.group2 = group2
test_result_list.append(
Annotation((group_struct1, group_struct2),
result,
formatter=self.pvalue_format))
# Perform other types of correction methods for multiple testing
self._apply_comparisons_correction(test_result_list)
return test_result_list
def test_missing_formatter(self):
res = StatResult("Custom test", None, pval=0.05, stat=None,
stat_str=None)
with self.assertRaisesRegex(ValueError, "PValueFormat"):
annotation = Annotation(("group1", "group2"),
res)
print(annotation.text)
def set_custom_annotations(self, text_annot_custom):
"""
:param text_annot_custom: List of strings to annotate for each
`pair`
"""
self._check_has_plotter()
self._check_correct_number_custom_annotations(text_annot_custom)
self.annotations = [Annotation(struct, text) for
struct, text in zip(self._struct_pairs,
text_annot_custom)]
self.show_test_name = False
self._deactivate_configured_warning()
return self
def test_text_string(self):
annotation_text = "p=0.05"
annotation = Annotation(("group1", "group2"),
annotation_text)
self.assertEqual(annotation.text, annotation_text)
self.assertEqual(annotation.formatted_output, annotation_text)