101 pval selection

.github/workflows/python-package.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9"]
+        python-version: ["3.8", "3.9", "3.10"]
 
     steps:
     - uses: actions/checkout@v2

moonstone/analysis/differential_analysis.py

@@ -78,7 +78,7 @@ def test_multiple_features(self, feature, test_to_use):
             list_ofgroups = []
             for variable in variable_dic:
                 list_ofgroups.append(variable_dic[variable][self.full_table.columns[family]])
-            #test = self.tests_functions_used[test_to_use](*np.asarray(list_ofgroups))
+            # test = self.tests_functions_used[test_to_use](*np.asarray(list_ofgroups))
             test = self.tests_functions_used[test_to_use](*list_ofgroups)  # works for kruskal and one way anova
             features.append(feature)
             taxons.append(self.full_table.columns[family])

moonstone/plot/counts.py

@@ -70,8 +70,8 @@ def plot_mean_distribution(
 
         mean_series = self.df.mean(axis=1)
         binned_mean = SeriesBinning(mean_series).binned_data
-        bar_fig = BarGraph(binned_mean, plotting_options, show=show, output_file=output_file)
-        bar_fig.plot_one_graph(plotting_options, show=show, output_file=output_file)
+        bar_fig = BarGraph(binned_mean)
+        bar_fig.plot_one_graph(plotting_options=plotting_options, show=show, output_file=output_file)
 
 
 class PlotTaxonomyCounts:

moonstone/plot/graphs/base.py

@@ -17,18 +17,9 @@ class BaseGraph(ABC):
     def __init__(
         self,
         data: Union[pd.Series, pd.DataFrame],
-        plotting_options: dict = None,
-        show: bool = True,
-        output_file: Union[bool, str] = False,
     ):
         """
         :param data: data to plot
-        :param show: set to False if you don't want to show the plot
-        :param output_file: name of the output file
-        :param plotting_options: options of plotting that will override the default setup \n
-                                 [!] Make sure the value given to an argument is of the right type \n
-                                 options allowed : 'log': `bool` ; 'colorbar': `[str, List[str]]` ;
-                                 'tickangle': `[int, float]`
         """
         self.data = data
 
@@ -236,7 +227,7 @@ def plot_one_graph(
             if groups:
                 filtered_df = self.data[self.data[group_col].isin(groups)]
                 filtered_df[group_col] = filtered_df[group_col].astype("category")
-                filtered_df[group_col].cat = filtered_df[group_col].cat.set_categories(groups)
+                filtered_df[group_col] = filtered_df[group_col].cat.set_categories(groups, ordered=True)
                 filtered_df = filtered_df.sort_values([group_col])
             else:
                 filtered_df = copy.deepcopy(self.data)

setup.py

@@ -9,19 +9,19 @@
     author='Kenzo-Hugo Hillion, Agnès Baud, Mariela Furstenheim, Sean Kennedy',
     author_email='kehillio@pasteur.fr',
     install_requires=[
-        'pandas==2.0.2',
-        'matplotlib==3.3.0',
-        'plotly==5.17.0',
-        'statsmodels==0.14.0',
-        'python-slugify==4.0.1',
-        'pyaml==20.4.0',
-        'numpy==1.24.3',
-        'scikit-bio==0.5.9',
-        'scikit-learn==1.3.1',
-        'hdmedians==0.14.2',
-        'cython==0.29.21',
-        'scipy==1.9.0'
+        'pandas>=2.0.2',
+        'matplotlib>=3.3.0',
+        'plotly>=5.17.0',
+        'statsmodels>=0.14.0',
+        'python-slugify>=4.0.1',
+        'pyaml>=20.4.0',
+        'numpy>=1.24.3',
+        'scikit-bio>=0.5.9',
+        'scikit-learn>=1.3.1',
+        'hdmedians>=0.14.2',
+        'cython>=0.29.21',
+        'scipy>=1.9.0'
     ],
     packages=find_packages(),
     entry_points={'console_scripts': ['moonstone=moonstone.main:run']},
-)
+)