add p separators for annotations

Signed-off-by: Florian Charlier <477844+trevismd@users.noreply.github.com>

Author: trevismd

CHANGELOG.md

@@ -1,4 +1,12 @@
 ## v0.7
+### v0.7.2
+### Features
+- Add option to capitalize "p" in annotations 
+  (PR [#172](https://github.com/trevismd/statannotations/pull/172) by 
+  [Pentabyteman](https://github.com/Pentabyteman))
+- Add option to change spacing in annotations 
+  (PR [#173](https://github.com/trevismd/statannotations/pull/173))
+
 ### v0.7.1
 #### Fixes
 - Fix minimum Python requirements in setup.py

coverage.svg

@@ -1,19 +1,21 @@
-from statannotations.stats.StatResult import StatResult
+from typing import Tuple, Union
 
 from statannotations.format_annotations import pval_annotation_text, \
     simple_text
+from statannotations.stats.StatResult import StatResult
 from statannotations.utils import DEFAULT, check_valid_text_format, \
     InvalidParametersError
 
 CONFIGURABLE_PARAMETERS = [
     'correction_format',
     'fontsize',
-    'pvalue_format_string',
     'simple_format_string',
     'text_format',
+    'pvalue_format_string',
     'pvalue_thresholds',
+    'p_capitalized',
+    'p_separators',
     'show_test_name',
-    'p_capitalized'
 ]
 
 
@@ -40,6 +42,7 @@ def __init__(self):
         self._correction_format = "{star} ({suffix})"
         self.show_test_name = True
         self.p_capitalized = False
+        self._p_separators = (" ", " ")
 
     def config(self, **parameters):
 
@@ -69,6 +72,30 @@ def text_format(self, text_format):
         check_valid_text_format(text_format)
         self._text_format = text_format
 
+    @property
+    def p_separators(self):
+        return {
+            (" ", " "): 'both',
+            ("", " "): 'after',
+            ("", ""): 'none',
+        }.get(self._p_separators, self._p_separators)
+
+    @p_separators.setter
+    def p_separators(self, p_separators: Union[bool, str, Tuple[str]] = True):
+        """
+        :param p_separators:
+            'both' (or True)(default), 'none' (or False), 'after',
+            or tuple[bool] for before and after
+        """
+        if isinstance(p_separators, tuple):
+            self._p_separators = p_separators
+        elif p_separators in {'none', False}:
+            self._p_separators = ("", "")
+        elif p_separators == 'after':
+            self._p_separators = ("", " ")
+        else:
+            self._p_separators = (" ", " ")
+
     def _get_pvalue_thresholds(self, pvalue_thresholds):
         if self._default_pvalue_thresholds:
             if self.text_format == "star":
@@ -179,10 +206,10 @@ def format_data(self, result):
                     else "")
 
             p_letter = "P" if self.p_capitalized else "p"
-
-            return ("{}{} = {}{}"
-                    .format('{}', p_letter, self.pvalue_format_string, '{}')
-                    .format(text, result.pvalue, result.significance_suffix))
+            equals = f"{self._p_separators[0]}={self._p_separators[1]}"
+            formatted_pvalue = self.pvalue_format_string.format(result.pvalue)
+            full_pvalue = f"{formatted_pvalue}{result.significance_suffix}"
+            return f"{text}{p_letter}{equals}{full_pvalue}"
 
         elif self.text_format == 'star':
             was_list = False
@@ -200,10 +227,10 @@ def format_data(self, result):
 
             return annotations[0]
 
-        # elif self.text_format == 'simple':
         else:
-            return simple_text(result, self.simple_format_string,
-                               self.pvalue_thresholds, self.show_test_name, self.p_capitalized)
+            return simple_text(
+                result, self.simple_format_string, self.pvalue_thresholds,
+                self.show_test_name, self.p_capitalized, self._p_separators)
 
     def get_configuration(self):
         return {key: getattr(self, key) for key in CONFIGURABLE_PARAMETERS}

statannotations/PValueFormat.py

@@ -1 +1 @@
-__version__ = "0.7.1"
+__version__ = "0.7.2"

statannotations/_version.py

@@ -1,8 +1,10 @@
-from statannotations.stats.StatResult import StatResult
-from typing import List
+from operator import itemgetter
+from typing import List, Tuple
+
 import numpy as np
 import pandas as pd
-from operator import itemgetter
+
+from statannotations.stats.StatResult import StatResult
 
 
 def pval_annotation_text(result: List[StatResult],
@@ -32,32 +34,38 @@ def pval_annotation_text(result: List[StatResult],
     return [(star, res) for star, res in zip(x_annot, result)]
 
 
-def simple_text(result: StatResult, pvalue_format, pvalue_thresholds,
-                short_test_name=True, p_capitalized=False) -> str:
+def simple_text(result: StatResult, pvalue_format: str,
+                pvalue_thresholds: List[list],
+                short_test_name: bool = True, p_capitalized: bool = False,
+                separators: Tuple[str] = (" ", " ")) -> str:
     """
     Generates simple text for test name and pvalue.
 
     :param result: StatResult instance
     :param pvalue_format: format string for pvalue
     :param pvalue_thresholds: String to display per pvalue range
     :param short_test_name: whether to display the test (short) name
+    :param p_capitalized: set True to show "P" instead of "p" in annotations
+    :param separators: separators for before and after '=' or '≤'
     :returns: simple annotation
 
     """
-    # Sort thresholds
     thresholds = sorted(pvalue_thresholds, key=lambda x: x[0])
 
     text = (f"{result.test_short_name} "
             if short_test_name and result.test_short_name
             else "")
 
     p_letter = "P" if p_capitalized else "p"
+    p_equals = f"{p_letter}{separators[0]}={separators[1]}"
+    p_lte = f"{p_letter}{separators[0]}≤{separators[1]}"
 
     for threshold in thresholds:
         if result.pvalue < threshold[0]:
-            pval_text = "{} ≤ {}".format(p_letter, threshold[1])
+            pval_text = f"{p_lte}{threshold[1]}"
             break
     else:
-        pval_text = "{} = {}".format(p_letter, pvalue_format).format(result.pvalue)
+        formatted_pvalue = pvalue_format.format(result.pvalue)
+        pval_text = f"{p_equals}{formatted_pvalue}"
 
     return result.adjust(text + pval_text)

statannotations/format_annotations.py

@@ -111,22 +111,26 @@ def test_print_pvalue_other(self):
 
     def test_get_configuration(self):
         pvalue_format = PValueFormat()
-        self.assertDictEqual(pvalue_format.get_configuration(),
-                             {'correction_format': '{star} ({suffix})',
-                              'fontsize': 'medium',
-                              'p_capitalized': False,
-                              '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"]]
-                              }
-                             )
+        self.assertDictEqual(
+            pvalue_format.get_configuration(),
+            {
+                'correction_format': '{star} ({suffix})',
+                'fontsize': 'medium',
+                'p_capitalized': False,
+                'p_separators': 'both',
+                'pvalue_format_string': '{:.3e}',
+                'pvalue_thresholds': [
+                    [1e-4, "****"],
+                    [1e-3, "***"],
+                    [1e-2, "**"],
+                    [0.05, "*"],
+                    [1, "ns"]
+                ],
+                'show_test_name': True,
+                'simple_format_string': '{:.2f}',
+                'text_format': 'star',
+            }
+        )
 
     def test_config_pvalue_thresholds(self):
         pvalue_format = PValueFormat()
@@ -138,7 +142,7 @@ def test_config_pvalue_thresholds(self):
                                  "      ns: 5.00e-02 < p <= 1.00e+00\n"
                                  " <= 0.05: 1.00e-03 < p <= 5.00e-02\n"
                                  "<= 0.001: p <= 1.00e-03\n\n")
-        
+
     def test_pvalue_simple_capitalized(self):
         self.annotator.configure(pvalue_format={"text_format": "simple",
                                                 "p_capitalized": True})
@@ -153,4 +157,40 @@ def test_pvalue_full_capitalized(self):
                                                 "pvalue_format_string": "{:.2f}"})
         annotations = self.annotator._get_results("auto", pvalues=self.pvalues)
         self.assertEqual(["P = 0.04", "P = 0.03", "P = 0.90"],
-                         [annotation.text for annotation in annotations])
+                         [annotation.text for annotation in annotations])
+
+    def test_pvalue_simple_separators(self):
+        self.annotator.configure(pvalue_format={"text_format": "simple"})
+        for separator, expected_results in [
+            (None, ["p ≤ 0.05", "p ≤ 0.05", "p = 0.90"]),
+            (True, ["p ≤ 0.05", "p ≤ 0.05", "p = 0.90"]),
+            ('both', ["p ≤ 0.05", "p ≤ 0.05", "p = 0.90"]),
+            ('none', ["p≤0.05", "p≤0.05", "p=0.90"]),
+            ('after', ["p≤ 0.05", "p≤ 0.05", "p= 0.90"]),
+        ]:
+            with self.subTest(separator=separator):
+                config = {"pvalue_format": {"p_separators": separator}}
+                self.annotator.configure(**config)
+                annotations = self.annotator._get_results("auto", pvalues=self.pvalues)
+                self.assertEqual(expected_results, [a.text for a in annotations])
+
+    def test_pvalue_full_separators(self):
+        self.annotator.configure(
+            pvalue_format={
+                "text_format": "full",
+                "show_test_name": False,
+                "pvalue_format_string": "{:.2f}"
+            },
+        )
+        for separator, expected_results in [
+            (None, ["p = 0.04", "p = 0.03", "p = 0.90"]),
+            (True, ["p = 0.04", "p = 0.03", "p = 0.90"]),
+            ('both', ["p = 0.04", "p = 0.03", "p = 0.90"]),
+            ('none', ["p=0.04", "p=0.03", "p=0.90"]),
+            ('after', ["p= 0.04", "p= 0.03", "p= 0.90"]),
+        ]:
+            with self.subTest(separator=separator):
+                config = {"pvalue_format": {"p_separators": separator}}
+                self.annotator.configure(**config)
+                annotations = self.annotator._get_results("auto", pvalues=self.pvalues)
+                self.assertEqual(expected_results, [a.text for a in annotations])