class TestAnnotator(unittest.TestCase):
"""Test validation of parameters"""
def setUp(self):
self.data = [[1, 2, 3], [2, 5, 7]]
self.data2 = pd.DataFrame([[1, 2], [2, 5], [3, 7]], columns=["X", "Y"])
self.ax = sns.boxplot(data=self.data)
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
self.pairs_for_df = [(("a", "blue"), ("b", "blue")),
(("a", "blue"), ("a", "red"))]
self.df.y = self.df.y.astype(float)
self.params_df = {
"data": self.df,
"x": "x",
"y": "y",
"hue": "color",
"order": ["a", "b"],
"hue_order": ['red', 'blue']}
def test_init_simple(self):
self.annot = Annotator(self.ax, [(0, 1)], data=self.data)
def test_init_df(self):
self.ax = sns.boxplot(**self.params_df)
self.annot = Annotator(self.ax, pairs=self.pairs_for_df,
**self.params_df)
def test_init_barplot(self):
ax = sns.barplot(data=self.data)
self.annot = Annotator(ax, [(0, 1)], plot="barplot", data=self.data)
def test_test_name_provided(self):
self.test_init_simple()
with self.assertRaisesRegex(ValueError, "test"):
self.annot.apply_test()
def test_unmatched_x_in_box_pairs_without_hue(self):
with self.assertRaisesRegex(ValueError, "(specified in `pairs`)"):
self.annot = Annotator(self.ax, [(0, 2)], data=self.data)
def test_order_in_x(self):
with self.assertRaisesRegex(ValueError, "(specified in `order`)"):
self.annot = Annotator(self.ax, [(0, 2)], data=self.data,
order=[0, 1, 2])
def test_working_hue_orders(self):
self.annot = Annotator(self.ax, [(("a", "blue"), ("b", "blue"))],
data=self.df, x="x", y="y",
order=["a", "b"], hue='color',
hue_order=['red', 'blue'])
def test_unmatched_hue_in_hue_order(self):
with self.assertRaisesRegex(ValueError, "(specified in `hue_order`)"):
self.annot = Annotator(self.ax, [(("a", "blue"), ("b", "blue"))],
data=self.df, x="x", y="y",
order=["a", "b"], hue='color',
hue_order=['red', 'yellow'])
def test_unmatched_hue_in_box_pairs(self):
with self.assertRaisesRegex(ValueError, "(specified in `pairs`)"):
self.annot = Annotator(self.ax, [(("a", "yellow"), ("b", "blue"))],
data=self.df, x="x", y="y",
order=["a", "b"], hue='color',
hue_order=['red', 'blue'])
def test_unmatched_x_in_box_pairs_with_hue(self):
with self.assertRaisesRegex(ValueError, "(specified in `pairs`)"):
self.annot = Annotator(self.ax, [(("c", "blue"), ("b", "blue"))],
data=self.df, x="x", y="y",
order=["a", "b"], hue='color',
hue_order=['red', 'blue'])
def test_location(self):
self.test_init_simple()
with self.assertRaisesRegex(ValueError, "argument `loc`"):
self.annot.configure(loc="somewhere")
def test_unknown_parameter(self):
self.test_init_simple()
with self.assertRaisesRegex(
InvalidParametersError, re.escape("parameter(s) \"that\"")):
self.annot.configure(that="this")
def test_format(self):
self.test_init_simple()
with self.assertRaisesRegex(ValueError, "argument `text_format`"):
self.annot.configure(pvalue_format={'text_format': 'that'})
def test_apply_comparisons_correction(self):
self.test_init_simple()
self.assertIsNone(self.annot._apply_comparisons_correction([]))
def test_correct_num_custom_annotations(self):
self.test_init_simple()
with self.assertRaisesRegex(ValueError, "same length"):
self.annot.set_custom_annotations(["One", "Two"])
def test_not_implemented_plot(self):
with self.assertRaises(NotImplementedError):
Annotator(self.ax, [(0, 1)], data=self.data, plot="thatplot")
def test_reconfigure_alpha(self):
self.test_init_simple()
with self.assertWarnsRegex(UserWarning, "pvalue_thresholds"):
self.annot.configure(alpha=0.1)
self.annot.reset_configuration()
self.assertEqual(0.05, self.annot.alpha)
def test_reconfigure_alpha_with_thresholds(self):
self.test_init_simple()
self.annot.configure(alpha=0.1,
pvalue_format={"pvalue_thresholds": DEFAULT})
self.annot.reset_configuration()
self.assertEqual(0.05, self.annot.alpha)
def test_get_annotation_text_undefined(self):
self.test_init_simple()
self.assertIsNone(self.annot.get_annotations_text())
def test_get_annotation_text_calculated(self):
self.test_init_simple()
self.annot.configure(test="Mann-Whitney", verbose=2)
self.annot.apply_test()
self.assertEqual(["ns"], self.annot.get_annotations_text())
def test_get_annotation_text_in_input_order(self):
self.test_init_df()
self.annot.configure(test="Mann-Whitney", text_format="simple")
self.annot.apply_test()
expected = (['M.W.W. p = 0.25', 'M.W.W. p = 0.67']
if version.parse(scipy.__version__) < version.parse("1.7")
else ['M.W.W. p = 0.33', 'M.W.W. p = 1.00'])
self.assertEqual(expected, self.annot.get_annotations_text())
def test_init_df_inverted(self):
box_pairs = self.pairs_for_df[::-1]
self.ax = sns.boxplot(**self.params_df)
self.annot = Annotator(self.ax, pairs=box_pairs, **self.params_df)
def test_get_annotation_text_in_input_order_inverted(self):
self.test_init_df_inverted()
self.annot.configure(test="Mann-Whitney", text_format="simple")
self.annot.apply_test()
expected = (['M.W.W. p = 0.67', 'M.W.W. p = 0.25']
if version.parse(scipy.__version__) < version.parse("1.7")
else ['M.W.W. p = 1.00', 'M.W.W. p = 0.33'])
self.assertEqual(expected, self.annot.get_annotations_text())
def test_apply_no_apply_warns(self):
self.test_init_df_inverted()
self.annot.configure(test="Mann-Whitney", text_format="simple")
self.annot.apply_and_annotate()
self.ax = sns.boxplot(**self.params_df)
self.annot.new_plot(self.ax, self.pairs_for_df, **self.params_df)
self.annot.configure(test="Levene", text_format="simple")
with self.assertWarns(UserWarning):
self.annot.annotate()
def test_apply_apply_no_warns(self):
self.test_init_df_inverted()
self.annot.configure(test="Mann-Whitney", text_format="simple")
self.annot.apply_and_annotate()
self.ax = sns.boxplot(**self.params_df)
self.annot.new_plot(self.ax, self.pairs_for_df, **self.params_df)
self.annot.configure(test="Mann-Whitney-gt", text_format="simple")
self.annot.apply_and_annotate()
def test_valid_parameters_df_data_only(self):
self.ax = sns.boxplot(ax=self.ax, data=self.data2)
annot = Annotator(self.ax, pairs=[("X", "Y")],
data=self.data2)
annot.configure(test="Mann-Whitney").apply_and_annotate()
def test_comparisons_correction_by_name(self):
self.ax = sns.boxplot(ax=self.ax, data=self.data2)
annot = Annotator(self.ax, pairs=[("X", "Y")],
data=self.data2)
annot.configure(test="Mann-Whitney", comparisons_correction="BH")
annot.apply_and_annotate()
def test_empty_annotator_wo_new_plot_raises(self):
annot = Annotator.get_empty_annotator()
with self.assertRaises(RuntimeError):
annot.configure(test="Mann-Whitney")
def test_empty_annotator_then_new_plot_ok(self):
annot = Annotator.get_empty_annotator()
self.ax = sns.boxplot(ax=self.ax, data=self.data2)
annot.new_plot(self.ax, pairs=[("X", "Y")],
data=self.data2)
annot.configure(test="Mann-Whitney")
def test_ensure_ax_operation_format_args_not_ok(self):
with self.assertRaises(ValueError):
_ensure_ax_operation_format(["func", "param", None])
def test_ensure_ax_operation_format_op_not_ok(self):
with self.assertRaises(ValueError):
_ensure_ax_operation_format(["func", ["param"]])
def test_ensure_ax_operation_format_kwargs_not_ok(self):
with self.assertRaises(ValueError):
_ensure_ax_operation_format(["func", ["param"], {"that"}])
def test_ensure_ax_operation_format_func_not_ok(self):
with self.assertRaises(ValueError):
_ensure_ax_operation_format([sum, ["param"], {"that": "this"}])
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