Merge pull request #343 from MannLabs/fix_if_condition_dev

Fix if condition dev
MannLabs · Sep 20, 2024 · 6222756 · 6222756
2 parents 68dbd34 + 985719d
commit 6222756
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Showing 6 changed files with 16 additions and 3 deletions.
diff --git a/alphastats/gui/pages/05_GPT.py b/alphastats/gui/pages/05_GPT.py
diff --git a/alphastats/gui/utils/analysis_helper.py b/alphastats/gui/utils/analysis_helper.py
@@ -116,8 +116,19 @@ def gui_volcano_plot_differential_expression_analysis(
     """
     initalize volcano plot object with differential expression analysis results
     """
+    dataset = st.session_state[StateKeys.DATASET]
+
+    # TODO this is just a quickfix, a simple interface needs to be provided by DataSet
     volcano_plot = VolcanoPlot(
-        dataset=st.session_state[StateKeys.DATASET], **chosen_parameter_dict, plot=False
+        mat=dataset.mat,
+        rawinput=dataset.rawinput,
+        metadata=dataset.metadata,
+        sample=dataset.sample,
+        index_column=dataset.index_column,
+        gene_names=dataset._gene_names,
+        preprocessing_info=dataset.preprocessing_info,
+        **chosen_parameter_dict,
+        plot=False,
     )
     volcano_plot._perform_differential_expression_analysis()
     volcano_plot._add_hover_data_columns()

diff --git a/alphastats/gui/utils/options.py b/alphastats/gui/utils/options.py
@@ -1,3 +1,4 @@
+from alphastats import SpectronautLoader
 from alphastats.gui.utils.ui_helper import StateKeys
 from alphastats.loader.AlphaPeptLoader import AlphaPeptLoader
 from alphastats.loader.DIANNLoader import DIANNLoader

diff --git a/alphastats/gui/utils/overview_helper.py b/alphastats/gui/utils/overview_helper.py
@@ -2,6 +2,7 @@
 import streamlit as st
 
 from alphastats.DataSet import DataSet
+from alphastats.DataSet_Preprocess import PreprocessingStateKeys
 from alphastats.gui.utils.ui_helper import StateKeys, convert_df
 
 

diff --git a/alphastats/plots/VolcanoPlot.py b/alphastats/plots/VolcanoPlot.py
@@ -209,7 +209,7 @@ def _sam(self):  # TODO duplicated?
 
         transposed = self.mat.transpose()
 
-        if self.preprocessing_info[PreprocessingStateKeys.LOG2_TRANSFORMED] is None:
+        if not self.preprocessing_info[PreprocessingStateKeys.LOG2_TRANSFORMED]:
             # needs to be lpog2 transformed for fold change calculations
             transposed = transposed.transform(lambda x: np.log2(x))
 

diff --git a/alphastats/statistics/DifferentialExpressionAnalysis.py b/alphastats/statistics/DifferentialExpressionAnalysis.py
@@ -109,7 +109,7 @@ def _sam(self) -> pd.DataFrame:  # TODO duplicated?
 
         transposed = self.mat.transpose()
 
-        if self.preprocessing_info[PreprocessingStateKeys.LOG2_TRANSFORMED] is None:
+        if not self.preprocessing_info[PreprocessingStateKeys.LOG2_TRANSFORMED]:
             # needs to be lpog2 transformed for fold change calculations
             transposed = transposed.transform(lambda x: np.log2(x))