def boxplot_with_test(data, x, y, pairs):
plotting_parameters = {'data': data, 'x': x, 'y': y}
pvalues = [
mannwhitneyu(data[data[x] == pair[0]][y],
data[data[x] == pair[1]][y]).pvalue for pair in pairs
]
ax = sns.boxplot(**plotting_parameters)
# Add annotations
annotator = Annotator(ax, pairs, **plotting_parameters)
annotator.set_pvalues(pvalues)
annotator.annotate()
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
plotting_parameters = {
'data': tmp,
'x': 'classe_mortalidade',
'y': ind,
'order': ['A', 'B', 'C']
}
#tmp[['classe_mortalidade', i]].groupby('classe_mortalidade').mean()
pvalues = []
for p in pairs:
pvalues.append(
stats.ttest_ind(
tmp.loc[tmp.classe_mortalidade == p[0], ind],
tmp.loc[tmp.classe_mortalidade == p[1],
ind]).pvalue)
formatted_pvalues = [f"p={p:.2e}" for p in pvalues]
ax = get_log_ax()
sns.boxplot(**plotting_parameters).set_title(
'mz:{:.2f} rt:{:.2f}'.format(*data[k][0].loc[
ind, ['row m/z', 'row retention time']].tolist()))
sns.stripplot(**plotting_parameters)
annotator = Annotator(ax, pairs, **plotting_parameters)
annotator.set_pvalues(pvalues)
#annotator.set_custom_annotations(formatted_pvalues)
annotator.annotate()
#plt.savefig("plot1A.png", bbox_inches='tight')
pdf.savefig()
plt.close()