- New: added 'half_same_trends' optional to extract the table of each…

… group has the same trend (all positive or all negative non-NA values) and at east 50% of the values are non-NA of the result of group-control in condition.

- Change: refined the layout of the setting window.

Docs/ChangeLog.md

@@ -1,3 +1,10 @@
+# Version: 1.118.1
+## Date: 2024-11-7
+### Changes:
+- New: added 'half_same_trends' optional to extract the table of each group has the same trend (all positive or all negative non-NA values) and at  east 50% of the values are non-NA of the result of group-control in condition.
+- Change: refined the layout of the setting window.
+
+
 # Version: 1.118.0
 ## Date: 2024-11-7
 ### Changes:

metax/gui/metax_gui/main_window.ui

@@ -246,7 +246,7 @@
                  <x>0</x>
                  <y>0</y>
                  <width>528</width>
-                 <height>595</height>
+                 <height>591</height>
                 </rect>
                </property>
                <attribute name="label">
@@ -4602,6 +4602,13 @@
                             <height>16777215</height>
                            </size>
                           </property>
+                          <property name="toolTip">
+                           <string>- 'all_sig': DataFrame containing all significant rows across all groups, Non-significant values are replaced with NA.
+- 'half_same_trends': DataFrame containing rows where each group has the same trend (all positive or all negative non-NA values) and at least 50% of the values are non-NA.
+- 'no_na': DataFrame containing rows with no NA values in each group.
+- 'same_trends': DataFrame containing rows with no NA values, and all values in each group follow the same trend (all positive or all negative).
+</string>
+                          </property>
                           <item>
                            <property name="text">
                             <string>all_sig</string>
@@ -4612,6 +4619,11 @@
                             <string>no_na</string>
                            </property>
                           </item>
+                          <item>
+                           <property name="text">
+                            <string>half_same_trends</string>
+                           </property>
+                          </item>
                           <item>
                            <property name="text">
                             <string>same_trends</string>
@@ -5701,7 +5713,7 @@
                            <x>0</x>
                            <y>0</y>
                            <width>996</width>
-                           <height>164</height>
+                           <height>160</height>
                           </rect>
                          </property>
                          <layout class="QGridLayout" name="gridLayout_68">
@@ -7482,7 +7494,7 @@
                         <x>0</x>
                         <y>0</y>
                         <width>1016</width>
-                        <height>166</height>
+                        <height>162</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_57">
@@ -9303,7 +9315,7 @@
                         <x>0</x>
                         <y>0</y>
                         <width>1016</width>
-                        <height>179</height>
+                        <height>177</height>
                        </rect>
                       </property>
                       <layout class="QGridLayout" name="gridLayout_66">
@@ -10437,7 +10449,7 @@
      <x>0</x>
      <y>0</y>
      <width>1122</width>
-     <height>21</height>
+     <height>23</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuTools">

metax/gui/metax_gui/setting_window.ui

@@ -17,61 +17,15 @@
    <item row="0" column="0">
     <widget class="QToolBox" name="toolBox">
      <property name="currentIndex">
-      <number>1</number>
+      <number>0</number>
      </property>
-     <widget class="QWidget" name="page">
-      <property name="geometry">
-       <rect>
-        <x>0</x>
-        <y>0</y>
-        <width>748</width>
-        <height>340</height>
-       </rect>
-      </property>
-      <attribute name="label">
-       <string>General</string>
-      </attribute>
-      <layout class="QGridLayout" name="gridLayout_3">
-       <item row="0" column="0">
-        <layout class="QGridLayout" name="gridLayout_2">
-         <item row="0" column="0">
-          <widget class="QCheckBox" name="checkBox_auto_check_update">
-           <property name="text">
-            <string>Auto Check Update</string>
-           </property>
-           <property name="checked">
-            <bool>true</bool>
-           </property>
-          </widget>
-         </item>
-         <item row="0" column="1">
-          <widget class="QRadioButton" name="radioButton_update_stable">
-           <property name="text">
-            <string>Stable</string>
-           </property>
-           <property name="checked">
-            <bool>true</bool>
-           </property>
-          </widget>
-         </item>
-         <item row="0" column="2">
-          <widget class="QRadioButton" name="radioButton_update_beta">
-           <property name="text">
-            <string>Beta</string>
-           </property>
-          </widget>
-         </item>
-        </layout>
-       </item>
-      </layout>
-     </widget>
      <widget class="QWidget" name="page_2">
       <property name="geometry">
        <rect>
         <x>0</x>
         <y>0</y>
         <width>748</width>
-        <height>340</height>
+        <height>367</height>
        </rect>
       </property>
       <attribute name="label">
@@ -739,7 +693,7 @@
         <x>0</x>
         <y>0</y>
         <width>748</width>
-        <height>340</height>
+        <height>367</height>
        </rect>
       </property>
       <attribute name="label">
@@ -778,6 +732,37 @@
          </item>
         </layout>
        </item>
+       <item row="0" column="0" colspan="2">
+        <layout class="QGridLayout" name="gridLayout_2">
+         <item row="0" column="0">
+          <widget class="QCheckBox" name="checkBox_auto_check_update">
+           <property name="text">
+            <string>Auto Check Update</string>
+           </property>
+           <property name="checked">
+            <bool>true</bool>
+           </property>
+          </widget>
+         </item>
+         <item row="0" column="1">
+          <widget class="QRadioButton" name="radioButton_update_stable">
+           <property name="text">
+            <string>Stable</string>
+           </property>
+           <property name="checked">
+            <bool>true</bool>
+           </property>
+          </widget>
+         </item>
+         <item row="0" column="2">
+          <widget class="QRadioButton" name="radioButton_update_beta">
+           <property name="text">
+            <string>Beta</string>
+           </property>
+          </widget>
+         </item>
+        </layout>
+       </item>
       </layout>
      </widget>
     </widget>

metax/gui/metax_gui/ui_main_window.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# Form implementation generated from reading ui file 'c:\Users\Qing\OneDrive - University of Ottawa\code\TaxaFunc\MetaX\metax\gui\metax_gui\main_window.ui'
+# Form implementation generated from reading ui file 'c:\Users\max\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, 595))
+        self.page_2.setGeometry(QtCore.QRect(0, 0, 528, 591))
         self.page_2.setObjectName("page_2")
         self.gridLayout_27 = QtWidgets.QGridLayout(self.page_2)
         self.gridLayout_27.setObjectName("gridLayout_27")
@@ -2309,6 +2309,7 @@ def setupUi(self, metaX_main):
         self.comboBox_cross_3_level_plot_df_type.addItem("")
         self.comboBox_cross_3_level_plot_df_type.addItem("")
         self.comboBox_cross_3_level_plot_df_type.addItem("")
+        self.comboBox_cross_3_level_plot_df_type.addItem("")
         self.gridLayout_51.addWidget(self.comboBox_cross_3_level_plot_df_type, 3, 4, 1, 1)
         self.checkBox_cross_3_level_plot_remove_zero_col = QtWidgets.QCheckBox(self.scrollAreaWidgetContents_3)
         sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Fixed)
@@ -2901,7 +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, 164))
+        self.scrollAreaWidgetContents_4.setGeometry(QtCore.QRect(0, 0, 996, 160))
         self.scrollAreaWidgetContents_4.setObjectName("scrollAreaWidgetContents_4")
         self.gridLayout_68 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_4)
         self.gridLayout_68.setObjectName("gridLayout_68")
@@ -3847,7 +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, 166))
+        self.scrollAreaWidgetContents_6.setGeometry(QtCore.QRect(0, 0, 1016, 162))
         self.scrollAreaWidgetContents_6.setObjectName("scrollAreaWidgetContents_6")
         self.gridLayout_57 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_6)
         self.gridLayout_57.setObjectName("gridLayout_57")
@@ -4856,7 +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, 179))
+        self.scrollAreaWidgetContents_8.setGeometry(QtCore.QRect(0, 0, 1016, 177))
         self.scrollAreaWidgetContents_8.setObjectName("scrollAreaWidgetContents_8")
         self.gridLayout_66 = QtWidgets.QGridLayout(self.scrollAreaWidgetContents_8)
         self.gridLayout_66.setObjectName("gridLayout_66")
@@ -5425,7 +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, 21))
+        self.menuBar.setGeometry(QtCore.QRect(0, 0, 1122, 23))
         self.menuBar.setObjectName("menuBar")
         self.menuTools = QtWidgets.QMenu(self.menuBar)
         self.menuTools.setObjectName("menuTools")
@@ -5871,9 +5872,15 @@ def retranslateUi(self, metaX_main):
         self.label_139.setText(_translate("metaX_main", "To"))
         self.label_58.setText(_translate("metaX_main", "Top Number"))
         self.label_141.setText(_translate("metaX_main", "Plot Type"))
+        self.comboBox_cross_3_level_plot_df_type.setToolTip(_translate("metaX_main", "- \'all_sig\': DataFrame containing all significant rows across all groups, Non-significant values are replaced with NA.\n"
+"- \'half_same_trends\': DataFrame containing rows where each group has the same trend (all positive or all negative non-NA values) and at least 50% of the values are non-NA.\n"
+"- \'no_na\': DataFrame containing rows with no NA values in each group.\n"
+"- \'same_trends\': DataFrame containing rows with no NA values, and all values in each group follow the same trend (all positive or all negative).\n"
+""))
         self.comboBox_cross_3_level_plot_df_type.setItemText(0, _translate("metaX_main", "all_sig"))
         self.comboBox_cross_3_level_plot_df_type.setItemText(1, _translate("metaX_main", "no_na"))
-        self.comboBox_cross_3_level_plot_df_type.setItemText(2, _translate("metaX_main", "same_trends"))
+        self.comboBox_cross_3_level_plot_df_type.setItemText(2, _translate("metaX_main", "half_same_trends"))
+        self.comboBox_cross_3_level_plot_df_type.setItemText(3, _translate("metaX_main", "same_trends"))
         self.checkBox_cross_3_level_plot_remove_zero_col.setText(_translate("metaX_main", "Remove Zero Col"))
         self.label_30.setText(_translate("metaX_main", "with"))
         self.comboBox_top_heatmap_scale_method.setItemText(0, _translate("metaX_main", "maxmin"))

metax/gui/metax_gui/ui_setting_window.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-# Form implementation generated from reading ui file 'c:\Users\Qing\OneDrive - University of Ottawa\code\TaxaFunc\MetaX\metax\gui\metax_gui\setting_window.ui'
+# Form implementation generated from reading ui file 'c:\Users\max\OneDrive - University of Ottawa\code\TaxaFunc\MetaX\metax\gui\metax_gui\setting_window.ui'
 #
 # Created by: PyQt5 UI code generator 5.15.9
 #
@@ -19,28 +19,8 @@ def setupUi(self, Settings):
         self.gridLayout.setObjectName("gridLayout")
         self.toolBox = QtWidgets.QToolBox(Settings)
         self.toolBox.setObjectName("toolBox")
-        self.page = QtWidgets.QWidget()
-        self.page.setGeometry(QtCore.QRect(0, 0, 748, 340))
-        self.page.setObjectName("page")
-        self.gridLayout_3 = QtWidgets.QGridLayout(self.page)
-        self.gridLayout_3.setObjectName("gridLayout_3")
-        self.gridLayout_2 = QtWidgets.QGridLayout()
-        self.gridLayout_2.setObjectName("gridLayout_2")
-        self.checkBox_auto_check_update = QtWidgets.QCheckBox(self.page)
-        self.checkBox_auto_check_update.setChecked(True)
-        self.checkBox_auto_check_update.setObjectName("checkBox_auto_check_update")
-        self.gridLayout_2.addWidget(self.checkBox_auto_check_update, 0, 0, 1, 1)
-        self.radioButton_update_stable = QtWidgets.QRadioButton(self.page)
-        self.radioButton_update_stable.setChecked(True)
-        self.radioButton_update_stable.setObjectName("radioButton_update_stable")
-        self.gridLayout_2.addWidget(self.radioButton_update_stable, 0, 1, 1, 1)
-        self.radioButton_update_beta = QtWidgets.QRadioButton(self.page)
-        self.radioButton_update_beta.setObjectName("radioButton_update_beta")
-        self.gridLayout_2.addWidget(self.radioButton_update_beta, 0, 2, 1, 1)
-        self.gridLayout_3.addLayout(self.gridLayout_2, 0, 0, 1, 1)
-        self.toolBox.addItem(self.page, "")
         self.page_2 = QtWidgets.QWidget()
-        self.page_2.setGeometry(QtCore.QRect(0, 0, 748, 340))
+        self.page_2.setGeometry(QtCore.QRect(0, 0, 748, 367))
         self.page_2.setObjectName("page_2")
         self.gridLayout_4 = QtWidgets.QGridLayout(self.page_2)
         self.gridLayout_4.setObjectName("gridLayout_4")
@@ -303,7 +283,7 @@ def setupUi(self, Settings):
         self.gridLayout_4.addLayout(self.gridLayout_12, 2, 3, 1, 1)
         self.toolBox.addItem(self.page_2, "")
         self.page_3 = QtWidgets.QWidget()
-        self.page_3.setGeometry(QtCore.QRect(0, 0, 748, 340))
+        self.page_3.setGeometry(QtCore.QRect(0, 0, 748, 367))
         self.page_3.setObjectName("page_3")
         self.gridLayout_11 = QtWidgets.QGridLayout(self.page_3)
         self.gridLayout_11.setObjectName("gridLayout_11")
@@ -321,20 +301,30 @@ def setupUi(self, Settings):
         self.label_24.setObjectName("label_24")
         self.gridLayout_10.addWidget(self.label_24, 0, 0, 1, 1)
         self.gridLayout_11.addLayout(self.gridLayout_10, 1, 1, 1, 1)
+        self.gridLayout_2 = QtWidgets.QGridLayout()
+        self.gridLayout_2.setObjectName("gridLayout_2")
+        self.checkBox_auto_check_update = QtWidgets.QCheckBox(self.page_3)
+        self.checkBox_auto_check_update.setChecked(True)
+        self.checkBox_auto_check_update.setObjectName("checkBox_auto_check_update")
+        self.gridLayout_2.addWidget(self.checkBox_auto_check_update, 0, 0, 1, 1)
+        self.radioButton_update_stable = QtWidgets.QRadioButton(self.page_3)
+        self.radioButton_update_stable.setChecked(True)
+        self.radioButton_update_stable.setObjectName("radioButton_update_stable")
+        self.gridLayout_2.addWidget(self.radioButton_update_stable, 0, 1, 1, 1)
+        self.radioButton_update_beta = QtWidgets.QRadioButton(self.page_3)
+        self.radioButton_update_beta.setObjectName("radioButton_update_beta")
+        self.gridLayout_2.addWidget(self.radioButton_update_beta, 0, 2, 1, 1)
+        self.gridLayout_11.addLayout(self.gridLayout_2, 0, 0, 1, 2)
         self.toolBox.addItem(self.page_3, "")
         self.gridLayout.addWidget(self.toolBox, 0, 0, 1, 1)
 
         self.retranslateUi(Settings)
-        self.toolBox.setCurrentIndex(1)
+        self.toolBox.setCurrentIndex(0)
         QtCore.QMetaObject.connectSlotsByName(Settings)
 
     def retranslateUi(self, Settings):
         _translate = QtCore.QCoreApplication.translate
         Settings.setWindowTitle(_translate("Settings", "Settings"))
-        self.checkBox_auto_check_update.setText(_translate("Settings", "Auto Check Update"))
-        self.radioButton_update_stable.setText(_translate("Settings", "Stable"))
-        self.radioButton_update_beta.setText(_translate("Settings", "Beta"))
-        self.toolBox.setItemText(self.toolBox.indexOf(self.page), _translate("Settings", "General"))
         self.label_4.setText(_translate("Settings", "Taxa-Functions Link Network"))
         self.label_11.setText(_translate("Settings", "Line Width"))
         self.label_15.setToolTip(_translate("Settings", "The larger the value the greater the repulsion"))
@@ -418,4 +408,7 @@ def retranslateUi(self, Settings):
         self.comboBox_protein_infer_greedy_mode.setItemText(0, _translate("Settings", "fast"))
         self.comboBox_protein_infer_greedy_mode.setItemText(1, _translate("Settings", "normal"))
         self.label_24.setText(_translate("Settings", "Greedy Mode in Razor Method"))
+        self.checkBox_auto_check_update.setText(_translate("Settings", "Auto Check Update"))
+        self.radioButton_update_stable.setText(_translate("Settings", "Stable"))
+        self.radioButton_update_beta.setText(_translate("Settings", "Beta"))
         self.toolBox.setItemText(self.toolBox.indexOf(self.page_3), _translate("Settings", "Others"))