- Change: changed the "Sum normalization" to "Percentages Scaling" in…

… the data preprossing part to avoid the confusion with the normalization method.

Docs/ChangeLog.md

@@ -1,3 +1,9 @@
+# Version: 1.118.2
+## Date: 2024-11-8
+### Changes:
+- Change: changed the "Sum normalization" to "Percentages Scaling" in the data preprossing part to avoid the confusion with the normalization method.
+
+
 # Version: 1.118.1
 ## Date: 2024-11-7
 ### Changes:

metax/gui/main_gui.py

@@ -2674,7 +2674,7 @@ def set_multi_table(self, restore_taxafunc=False,  saved_obj=None):
                     "Standard Scaling (Z-Score)": "zscore",
                     "Min-Max Scaling": "minmax",
                     "Pareto Scaling": "pareto",
-                    "Normalization by sum": "sum",
+                    "Percentages Scaling": "percentage",
                 }
                 normalize_method = normalize_dict[normalize_method]
                 transform_method = transform_dict[transform_method]

metax/gui/metax_gui/main_window.ui

@@ -46,7 +46,7 @@
            <enum>Qt::LeftToRight</enum>
           </property>
           <property name="currentIndex">
-           <number>4</number>
+           <number>2</number>
           </property>
           <property name="documentMode">
            <bool>false</bool>
@@ -246,7 +246,7 @@
                  <x>0</x>
                  <y>0</y>
                  <width>528</width>
-                 <height>591</height>
+                 <height>595</height>
                 </rect>
                </property>
                <attribute name="label">
@@ -976,7 +976,7 @@
                 </item>
                 <item>
                  <property name="text">
-                  <string>Normalization by sum</string>
+                  <string>Percentages Scaling</string>
                  </property>
                 </item>
                </widget>
@@ -5713,7 +5713,7 @@
                            <x>0</x>
                            <y>0</y>
                            <width>996</width>
-                           <height>160</height>
+                           <height>164</height>
                           </rect>
                          </property>
                          <layout class="QGridLayout" name="gridLayout_68">
@@ -7494,7 +7494,7 @@
                         <x>0</x>
                         <y>0</y>
                         <width>1016</width>
-                        <height>162</height>
+                        <height>166</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_57">
@@ -9315,7 +9315,7 @@
                         <x>0</x>
                         <y>0</y>
                         <width>1016</width>
-                        <height>177</height>
+                        <height>179</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_66">
@@ -10449,7 +10449,7 @@
      <x>0</x>
      <y>0</y>
      <width>1122</width>
-     <height>23</height>
+     <height>21</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuTools">

metax/gui/metax_gui/ui_main_window.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# Form implementation generated from reading ui file 'c:\Users\max\OneDrive - University of Ottawa\code\TaxaFunc\MetaX\metax\gui\metax_gui\main_window.ui'
+# Form implementation generated from reading ui file 'c:\Users\Qing\OneDrive - University of Ottawa\code\TaxaFunc\MetaX\metax\gui\metax_gui\main_window.ui'
 #
 # Created by: PyQt5 UI code generator 5.15.9
 #
@@ -147,7 +147,7 @@ def setupUi(self, metaX_main):
         self.toolBox_2.setMaximumSize(QtCore.QSize(1677, 16777215))
         self.toolBox_2.setObjectName("toolBox_2")
         self.page_2 = QtWidgets.QWidget()
-        self.page_2.setGeometry(QtCore.QRect(0, 0, 528, 591))
+        self.page_2.setGeometry(QtCore.QRect(0, 0, 528, 595))
         self.page_2.setObjectName("page_2")
         self.gridLayout_27 = QtWidgets.QGridLayout(self.page_2)
         self.gridLayout_27.setObjectName("gridLayout_27")
@@ -2902,7 +2902,7 @@ def setupUi(self, metaX_main):
         self.scrollArea_3.setWidgetResizable(True)
         self.scrollArea_3.setObjectName("scrollArea_3")
         self.scrollAreaWidgetContents_4 = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents_4.setGeometry(QtCore.QRect(0, 0, 996, 160))
+        self.scrollAreaWidgetContents_4.setGeometry(QtCore.QRect(0, 0, 996, 164))
         self.scrollAreaWidgetContents_4.setObjectName("scrollAreaWidgetContents_4")
         self.gridLayout_68 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_4)
         self.gridLayout_68.setObjectName("gridLayout_68")
@@ -3848,7 +3848,7 @@ def setupUi(self, metaX_main):
         self.scrollArea_5.setWidgetResizable(True)
         self.scrollArea_5.setObjectName("scrollArea_5")
         self.scrollAreaWidgetContents_6 = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents_6.setGeometry(QtCore.QRect(0, 0, 1016, 162))
+        self.scrollAreaWidgetContents_6.setGeometry(QtCore.QRect(0, 0, 1016, 166))
         self.scrollAreaWidgetContents_6.setObjectName("scrollAreaWidgetContents_6")
         self.gridLayout_57 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_6)
         self.gridLayout_57.setObjectName("gridLayout_57")
@@ -4857,7 +4857,7 @@ def setupUi(self, metaX_main):
         self.scrollArea_7.setWidgetResizable(True)
         self.scrollArea_7.setObjectName("scrollArea_7")
         self.scrollAreaWidgetContents_8 = QtWidgets.QWidget()
-        self.scrollAreaWidgetContents_8.setGeometry(QtCore.QRect(0, 0, 1016, 177))
+        self.scrollAreaWidgetContents_8.setGeometry(QtCore.QRect(0, 0, 1016, 179))
         self.scrollAreaWidgetContents_8.setObjectName("scrollAreaWidgetContents_8")
         self.gridLayout_66 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_8)
         self.gridLayout_66.setObjectName("gridLayout_66")
@@ -5426,7 +5426,7 @@ def setupUi(self, metaX_main):
         self.statusbar.setObjectName("statusbar")
         metaX_main.setStatusBar(self.statusbar)
         self.menuBar = QtWidgets.QMenuBar(metaX_main)
-        self.menuBar.setGeometry(QtCore.QRect(0, 0, 1122, 23))
+        self.menuBar.setGeometry(QtCore.QRect(0, 0, 1122, 21))
         self.menuBar.setObjectName("menuBar")
         self.menuTools = QtWidgets.QMenu(self.menuBar)
         self.menuTools.setObjectName("menuTools")
@@ -5492,7 +5492,7 @@ def setupUi(self, metaX_main):
 
         self.retranslateUi(metaX_main)
         self.stackedWidget.setCurrentIndex(0)
-        self.tabWidget_TaxaFuncAnalyzer.setCurrentIndex(4)
+        self.tabWidget_TaxaFuncAnalyzer.setCurrentIndex(2)
         self.toolBox_2.setCurrentIndex(0)
         self.tabWidget_4.setCurrentIndex(0)
         self.tabWidget_3.setCurrentIndex(3)
@@ -5639,7 +5639,7 @@ def retranslateUi(self, metaX_main):
         self.comboBox_set_data_normalization.setItemText(3, _translate("metaX_main", "Min-Max Scaling"))
         self.comboBox_set_data_normalization.setItemText(4, _translate("metaX_main", "Pareto Scaling"))
         self.comboBox_set_data_normalization.setItemText(5, _translate("metaX_main", "Mean centering"))
-        self.comboBox_set_data_normalization.setItemText(6, _translate("metaX_main", "Normalization by sum"))
+        self.comboBox_set_data_normalization.setItemText(6, _translate("metaX_main", "Percentages Scaling"))
         self.comboBox_remove_batch_effect.setItemText(0, _translate("metaX_main", "None"))
         self.label_41.setText(_translate("metaX_main", "Data Normalization"))
         self.label_43.setText(_translate("metaX_main", "Batch Effect Correction"))

metax/taxafunc_analyzer/analyzer_utils/data_preprocessing.py

@@ -118,7 +118,7 @@ def trace_shift(x):
             normalize_operations = {
                 'None': lambda x: x,
                 'mean': lambda x: x - x.mean(),
-                'sum': lambda x: x / (x.sum() + epsilon),
+                'percentage': lambda x: x / (x.sum() + epsilon) * 100,
                 'minmax': lambda x: (x - x.min()) / (x.max() - x.min()),
                 'zscore': lambda x: (x - x.mean()) / (x.std() + epsilon),
                 'pareto': lambda x: (x - x.mean()) / (np.sqrt(x.std() + epsilon)),
@@ -143,7 +143,7 @@ def trace_shift(x):
 
                 print(f'Data normalized by [{normalize_method}]')
             else:
-                raise ValueError('normalize_method must be in [None, mean, sum, minmax, zscore, pareto]')
+                raise ValueError(f'normalize_method must be in {list(normalize_operations.keys())}')
 
             # move the data to positive
             df_mat = df_mat - df_mat.min()
@@ -637,7 +637,7 @@ def data_preprocess(self, df: pd.DataFrame, normalize_method: str|None = None,
             - `None`: No normalization.
             - `trace_shift`: Trace shift normalization inspired by DirectLFQ.
             - `mean`: Mean normalization.
-            - `sum`: Sum normalization.
+            - `percentage`: Percentage normalization, then *100.
             - `minmax`: Min-max normalization.
             - `zscore`: Z-score normalization.
             - `pareto`: Pareto scaling.

metax/utils/version.py

@@ -1,2 +1,2 @@
-__version__ = '1.118.1'
+__version__ = '1.118.2'
 API_version = '3'

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "MetaXTools"
-version = "1.118.1"
+version = "1.118.2"
 description = "MetaXTools is a novel tool for linking peptide sequences with taxonomic and functional information in Metaproteomics."
 readme = "README_PyPi.md"
 license = { text = "NorthOmics" }