map scipy ttest functions with strings

MannLabs · Dec 17, 2024 · e734a34 · e734a34
1 parent d28e36c
commit e734a34
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Showing 2 changed files with 15 additions and 11 deletions.
diff --git a/alphastats/tl/differential_expression_analysis.py b/alphastats/tl/differential_expression_analysis.py
@@ -225,11 +225,11 @@ def _extend_validation(self, input_data: pd.DataFrame, parameters: dict):
         """
         super()._extend_validation(input_data, parameters)
         if parameters["test_fun"] not in [
-            scipy.stats.ttest_ind,
-            scipy.stats.ttest_rel,
+            "independent",
+            "paired",
         ]:
             raise ValueError(
-                "test_fun must be either scipy.stats.ttest_ind or scipy.stats.ttest_rel for t-test."
+                "test_fun must be either 'independent' for scipy.stats.ttest_ind or 'paired' for scipy.stats.ttest_rel."
             )
         if parameters["fdr_method"] not in ["bh", "by"]:
             raise ValueError("fdr_method must be one of 'bh', 'by'.")
@@ -258,7 +258,7 @@ def _statistical_test_fun(
         group1: list,
         group2: list,
         is_log2_transformed: bool,
-        test_fun: callable,
+        test_fun: str,
         fdr_method: str,
     ) -> pd.DataFrame:
         """Runs the t-test analysis and returns the result.
@@ -268,14 +268,19 @@ def _statistical_test_fun(
         group1 (list): The samples for group 1.
         group2 (list): The samples for group 2.
         is_log2_transformed (bool): Whether the data is log2 transformed.
-        test_fun (callable): The test function to use, scipy.stats.ttest_ind or scipy.stats.ttest_rel.
+        test_fun (str): The test function to use, independent for scipy.stats.ttest_ind or paired for scipy.stats.ttest_rel.
         fdr_method (str): The FDR method to use, 'bh' or 'by'.
 
         Returns:
         pd.DataFrame: The result of the analysis.
         """
         mat_transpose = input_data.loc[group1 + group2, :].transpose()
 
+        test_fun = {
+            "independent": scipy.stats.ttest_ind,
+            "paired": scipy.stats.ttest_rel,
+        }[test_fun]
+
         if not is_log2_transformed:
             mat_transpose = mat_transpose.transform(np.log2)
             mat_transpose = mat_transpose.replace([np.inf, -np.inf], np.nan)

diff --git a/tests/tl/test_differential_expression_analysis.py b/tests/tl/test_differential_expression_analysis.py
@@ -3,7 +3,6 @@
 import numpy as np
 import pandas as pd
 import pytest
-import scipy
 
 from alphastats.dataset.keys import Cols
 from alphastats.dataset.preprocessing import PreprocessingStateKeys
@@ -353,7 +352,7 @@ def test_dea_ttest_perform_runs():
     dea.perform(
         **TestableDifferentialExpressionAnalysisTwoGroups.valid_parameter_input,
         **{
-            DeaParameters.TEST_FUN: scipy.stats.ttest_ind,
+            DeaParameters.TEST_FUN: "independent",
             DeaParameters.FDR_METHOD: "bh",
             PreprocessingStateKeys.LOG2_TRANSFORMED: True,
         },
@@ -369,7 +368,7 @@ def test_dea_ttest_runs_log(mock_transform):
     dea.perform(
         **TestableDifferentialExpressionAnalysisTwoGroups.valid_parameter_input,
         **{
-            DeaParameters.TEST_FUN: scipy.stats.ttest_ind,
+            DeaParameters.TEST_FUN: "independent",
             DeaParameters.FDR_METHOD: "bh",
             PreprocessingStateKeys.LOG2_TRANSFORMED: False,
         },
@@ -383,12 +382,12 @@ def test_dea_ttest_validate_wrong_stats_method():
     dea = DifferentialExpressionAnalysisTTest(input_data)
     with pytest.raises(
         ValueError,
-        match="test_fun must be either scipy.stats.ttest_ind or scipy.stats.ttest_rel for t-test.",
+        match="test_fun must be either 'independent' for scipy.stats.ttest_ind or 'paired' for scipy.stats.ttest_rel.",
     ):
         dea.perform(
             **TestableDifferentialExpressionAnalysisTwoGroups.valid_parameter_input,
             **{
-                DeaParameters.TEST_FUN: float,
+                DeaParameters.TEST_FUN: "not defined",
                 DeaParameters.FDR_METHOD: "bh",
                 PreprocessingStateKeys.LOG2_TRANSFORMED: True,
             },
@@ -402,7 +401,7 @@ def test_dea_ttest_validate_wrong_fdr_method():
         dea.perform(
             **TestableDifferentialExpressionAnalysisTwoGroups.valid_parameter_input,
             **{
-                DeaParameters.TEST_FUN: scipy.stats.ttest_ind,
+                DeaParameters.TEST_FUN: "independent",
                 DeaParameters.FDR_METHOD: "unknown",
                 PreprocessingStateKeys.LOG2_TRANSFORMED: True,
             },