From a9f66b2925f7d9aee4e38e877367ed156b5ae3e3 Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Wed, 4 Sep 2024 13:02:41 +0200
Subject: [PATCH 1/2] Add `TTestStatistic`.

---
 src/gpsea/analysis/pscore/stats/__init__.py |  4 +-
 src/gpsea/analysis/pscore/stats/_stats.py   | 26 +++++++++-
 tests/analysis/pscore/test_stats.py         | 54 +++++++++++++++++++++
 3 files changed, 81 insertions(+), 3 deletions(-)
 create mode 100644 tests/analysis/pscore/test_stats.py

diff --git a/src/gpsea/analysis/pscore/stats/__init__.py b/src/gpsea/analysis/pscore/stats/__init__.py
index e46bfb5e4..0d3956fad 100644
--- a/src/gpsea/analysis/pscore/stats/__init__.py
+++ b/src/gpsea/analysis/pscore/stats/__init__.py
@@ -1,7 +1,7 @@
 from ._stats import PhenotypeScoreStatistic
-from ._stats import MannWhitneyStatistic
+from ._stats import MannWhitneyStatistic, TTestStatistic
 
 __all__ = [
     'PhenotypeScoreStatistic',
-    'MannWhitneyStatistic',
+    'MannWhitneyStatistic', 'TTestStatistic',
 ]
diff --git a/src/gpsea/analysis/pscore/stats/_stats.py b/src/gpsea/analysis/pscore/stats/_stats.py
index 01cfa4d92..80f09fa48 100644
--- a/src/gpsea/analysis/pscore/stats/_stats.py
+++ b/src/gpsea/analysis/pscore/stats/_stats.py
@@ -1,7 +1,7 @@
 import abc
 import typing
 
-from scipy.stats import mannwhitneyu
+from scipy.stats import mannwhitneyu, ttest_ind
 
 
 class PhenotypeScoreStatistic(metaclass=abc.ABCMeta):
@@ -42,3 +42,27 @@ def compute_pval(
         )
 
         return pval
+
+
+class TTestStatistic(PhenotypeScoreStatistic):
+    """
+    `TTestStatistic` is a wrapper around SciPy's
+    :func:`~scipy.stats.ttest_ind` function to apply
+    T test on 2 phenotype scores.
+
+    See :ref:`phenotype-score-stats` for an example usage.
+    """
+
+    def compute_pval(
+        self,
+        scores: typing.Collection[typing.Sequence[float]],
+    ) -> float:
+        assert len(scores) == 2, 'T test only supports 2 categories at this time'
+        
+        x, y = scores
+        res = ttest_ind(
+            a=x, b=y,
+            alternative='two-sided',
+        )
+
+        return res.pvalue
diff --git a/tests/analysis/pscore/test_stats.py b/tests/analysis/pscore/test_stats.py
new file mode 100644
index 000000000..42fdd2ba6
--- /dev/null
+++ b/tests/analysis/pscore/test_stats.py
@@ -0,0 +1,54 @@
+import typing
+import pytest
+
+from gpsea.analysis.pscore.stats import MannWhitneyStatistic, TTestStatistic
+
+
+class TestMannWhitneyStatistic:
+
+    @pytest.fixture(scope='class')
+    def statistic(self) -> MannWhitneyStatistic:
+        return MannWhitneyStatistic()
+
+    @pytest.mark.parametrize(
+        'x, y, expected',
+        [
+            ((1., 2., 3., ), (1., 2., 3., ), 1.),
+            ((11., 15, 8., 12.,), (4., 2., 3., 3.5, 4.,), 0.01945103333136247),
+        ]
+    )
+    def test_compute_pval(
+        self,
+        statistic: MannWhitneyStatistic,
+        x: typing.Sequence[float],
+        y: typing.Sequence[float],
+        expected: float,
+    ):
+        actual = statistic.compute_pval((x, y))
+
+        assert actual == pytest.approx(expected)
+
+
+class TestTTestStatistic:
+
+    @pytest.fixture(scope='class')
+    def statistic(self) -> TTestStatistic:
+        return TTestStatistic()
+
+    @pytest.mark.parametrize(
+        'x, y, expected',
+        [
+            ((1., 2., 3., ), (1., 2., 3., ), 1.),
+            ((11., 15, 8., 12.,), (4., 2., 3., 3.5, 4.,), 0.0004749950471148506),
+        ]
+    )
+    def test_compute_pval(
+        self,
+        statistic: TTestStatistic,
+        x: typing.Sequence[float],
+        y: typing.Sequence[float],
+        expected: float,
+    ):
+        actual = statistic.compute_pval((x, y))
+
+        assert actual == pytest.approx(expected)

From cda263f6a31443aa4c187a279c6a71dbfee41ceb Mon Sep 17 00:00:00 2001
From: Daniel Danis <daniel.gordon.danis@protonmail.com>
Date: Wed, 4 Sep 2024 13:08:42 +0200
Subject: [PATCH 2/2] Mention the `pscore.stats` module in the docs.

---
 docs/user-guide/stats.rst                 | 6 ++++++
 src/gpsea/analysis/pscore/stats/_stats.py | 2 --
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/docs/user-guide/stats.rst b/docs/user-guide/stats.rst
index 5a8717f3b..55757ef30 100644
--- a/docs/user-guide/stats.rst
+++ b/docs/user-guide/stats.rst
@@ -463,6 +463,12 @@ We will use :ref:`mann-whitney-u-test` as described above.
 >>> score_statistic = MannWhitneyStatistic()
 
 
+.. tip::
+
+   See :mod:`gpsea.analysis.pscore.stats` module for more statistical tests available
+   for using with phenotype scores.
+
+
 **Final analysis**
 
 We will put the final analysis together into :class:`~gpsea.analysis.pscore.PhenotypeScoreAnalysis`.
diff --git a/src/gpsea/analysis/pscore/stats/_stats.py b/src/gpsea/analysis/pscore/stats/_stats.py
index 80f09fa48..7a520e84c 100644
--- a/src/gpsea/analysis/pscore/stats/_stats.py
+++ b/src/gpsea/analysis/pscore/stats/_stats.py
@@ -49,8 +49,6 @@ class TTestStatistic(PhenotypeScoreStatistic):
     `TTestStatistic` is a wrapper around SciPy's
     :func:`~scipy.stats.ttest_ind` function to apply
     T test on 2 phenotype scores.
-
-    See :ref:`phenotype-score-stats` for an example usage.
     """
 
     def compute_pval(