class Test(unittest.TestCase):
"""Test that the annotations match the pvalues and format."""
def setUp(self) -> None:
self.df = pd.DataFrame.from_dict({
1: {
"x": "a",
"y": 15,
"color": "blue"
},
2: {
"x": "a",
"y": 16,
"color": "blue"
},
3: {
"x": "b",
"y": 17,
"color": "blue"
},
4: {
"x": "b",
"y": 18,
"color": "blue"
},
5: {
"x": "a",
"y": 15,
"color": "red"
},
6: {
"x": "a",
"y": 16,
"color": "red"
},
7: {
"x": "b",
"y": 17,
"color": "red"
},
8: {
"x": "b",
"y": 18,
"color": "red"
}
}).T
plotting = {"data": self.df, "x": "x", "y": "y", "hue": "color"}
self.ax = sns.boxplot(**plotting)
self.annotator = Annotator(self.ax,
pairs=[(("a", "blue"), ("a", "red")),
(("b", "blue"), ("b", "red")),
(("a", "blue"), ("b", "blue"))],
verbose=False,
**plotting)
self.pvalues = [0.03, 0.04, 0.9]
def test_format_simple(self):
self.annotator.configure(pvalue_format={"text_format": "simple"})
annotations = self.annotator._get_results("auto", pvalues=self.pvalues)
self.assertEqual(["p ≤ 0.05", "p ≤ 0.05", "p = 0.90"],
[annotation.text for annotation in annotations])
def test_format_simple_in_annotator(self):
self.annotator.configure(text_format="simple")
annotations = self.annotator._get_results("auto", pvalues=self.pvalues)
self.assertEqual(["p ≤ 0.05", "p ≤ 0.05", "p = 0.90"],
[annotation.text for annotation in annotations])
def test_wrong_parameter(self):
with self.assertRaisesRegex(InvalidParametersError,
re.escape('parameter(s) "that"')):
self.annotator.configure(pvalue_format={"that": "whatever"})
def test_format_string(self):
self.annotator.configure(text_format="simple",
pvalue_format_string="{:.3f}")
self.assertEqual("{:.3f}",
self.annotator.pvalue_format.pvalue_format_string)
annotations = self.annotator._get_results("auto", pvalues=self.pvalues)
self.assertEqual(["p ≤ 0.05", "p ≤ 0.05", "p = 0.900"],
[annotation.text for annotation in annotations])
def test_format_string_default(self):
self.annotator.configure(text_format="simple",
pvalue_format_string="{:.3f}")
self.annotator.pvalue_format.config(pvalue_format_string=DEFAULT)
annotations = self.annotator._get_results("auto", pvalues=self.pvalues)
self.assertEqual(["p ≤ 0.05", "p ≤ 0.05", "p = 0.90"],
[annotation.text for annotation in annotations])
@unittest.mock.patch('sys.stdout', new_callable=io.StringIO)
def assert_print_pvalue(self, pvalue_format, expected_output, mock_stdout):
pvalue_format.print_legend_if_used()
self.assertEqual(expected_output, mock_stdout.getvalue())
def test_print_pvalue_default(self):
pvalue_format = PValueFormat()
self.assert_print_pvalue(
pvalue_format, "p-value annotation legend:\n"
" ns: p <= 1.00e+00\n"
" *: 1.00e-02 < p <= 5.00e-02\n"
" **: 1.00e-03 < p <= 1.00e-02\n"
" ***: 1.00e-04 < p <= 1.00e-03\n"
" ****: p <= 1.00e-04\n\n")
def test_print_pvalue_star(self):
pvalue_format = PValueFormat()
pvalue_format.config(text_format="star")
self.assert_print_pvalue(
pvalue_format, "p-value annotation legend:\n"
" ns: p <= 1.00e+00\n"
" *: 1.00e-02 < p <= 5.00e-02\n"
" **: 1.00e-03 < p <= 1.00e-02\n"
" ***: 1.00e-04 < p <= 1.00e-03\n"
" ****: p <= 1.00e-04\n\n")
def test_print_pvalue_other(self):
pvalue_format = PValueFormat()
pvalue_format.config(text_format="simple")
self.assert_print_pvalue(pvalue_format, "")
def test_get_configuration(self):
pvalue_format = PValueFormat()
self.assertDictEqual(
pvalue_format.get_configuration(), {
'correction_format':
'{star} ({suffix})',
'fontsize':
'medium',
'pvalue_format_string':
'{:.3e}',
'show_test_name':
True,
'simple_format_string':
'{:.2f}',
'text_format':
'star',
'pvalue_thresholds': [[1e-4, "****"], [1e-3, "***"],
[1e-2, "**"], [0.05, "*"], [1, "ns"]]
})
def test_config_pvalue_thresholds(self):
pvalue_format = PValueFormat()
pvalue_format.config(pvalue_thresholds=[[0.001, "<= 0.001"],
[0.05, "<= 0.05"], [1, 'ns']])
self.assert_print_pvalue(
pvalue_format, "p-value annotation legend:\n"
" ns: p <= 1.00e+00\n"
" <= 0.05: 1.00e-03 < p <= 5.00e-02\n"
"<= 0.001: p <= 1.00e-03\n\n")
class Test(unittest.TestCase):
"""Test that the annotations match the pvalues and format."""
def setUp(self) -> None:
# noinspection DuplicatedCode
self.df = pd.DataFrame.from_dict(
{1: {'x': "a", 'y': 15, 'color': 'blue'},
2: {'x': "a", 'y': 16, 'color': 'blue'},
3: {'x': "b", 'y': 17, 'color': 'blue'},
4: {'x': "b", 'y': 18, 'color': 'blue'},
5: {'x': "a", 'y': 15, 'color': 'red'},
6: {'x': "a", 'y': 16, 'color': 'red'},
7: {'x': "b", 'y': 17, 'color': 'red'},
8: {'x': "b", 'y': 18, 'color': 'red'}
}).T
plotting = {
"data": self.df,
"x": "x",
"y": "y",
"hue": 'color'
}
self.ax = sns.boxplot(**plotting)
self.annotator = Annotator(
self.ax, pairs=[(("a", "blue"), ("a", "red")),
(("b", "blue"), ("b", "red")),
(("a", "blue"), ("b", "blue"))],
**plotting)
self.pvalues = [0.03, 0.04, 0.9]
def test_ns_without_correction_star(self):
annotations = self.annotator._get_results("auto", pvalues=self.pvalues)
self.assertEqual(["*", "*", "ns"],
[annotation.text for annotation in annotations])
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_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_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_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_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 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_reapply_annotations(self):
pass
