- New: Added an option in 'Help' menu to open the online Tutorial page.

- Change: Co-expression Network plot: Use the corelation value as the weight of the edge, and improve the layout of the plot.
- Fix: Fixed the bug of when plot the Taxa-Functions Network, the shape setting was not work withotu focus list.

Docs/ChangeLog.md

@@ -1,3 +1,10 @@
+# Version: 1.107.2
+## Date: 2024-06-16
+### Changes:
+- New: Added an option in 'Help' menu to open the online Tutorial page.
+- Change: Co-expression Network plot: Use the corelation value as the weight of the edge, and improve the layout of the plot.
+- Fix: Fixed the bug of when plot the Taxa-Functions Network, the shape setting was not work withotu focus list.
+
 # Version: 1.107.1
 ## Date: 2024-06-16
 ### Changes:

README.md

@@ -9,7 +9,15 @@ MetaX also features <u>statistical modules</u> and <u>plotting tools</u> for ana
 ## Taxa-Functions Linkage
 Linking Taxa and Functions in different levels of the hierarchy, and different functional categories. e.g., **Species-KO**, **Genus-CAZy**, **Phylum-EC**, etc.
 
-![OTF](./Docs/MetaX_Cookbook.assets/tf_link_net.png)
+- ![OTF](./Docs/MetaX_Cookbook.assets/tf_link_net.png)
+
+
+
+e.g. The **KEGG Pathways** linked to ***Roseburia hominis***
+
+- ![tf_link_net_2](./Docs/MetaX_Cookbook.assets/tf_link_net_2.png)
+
+
 
 ## Download
 ### `Desktop Version(Recommended)`:

utils/GUI.py

@@ -163,8 +163,8 @@ def __init__(self, MainWindow):
         self.tf_link_net_params_dict = {'taxa_shape': 'circle', 'func_shape': 'rect', 
                                         'taxa_color': '#374E55','taxa_focus_color': '#6A6599', 
                                         'func_color': '#DF8F44', 'func_focus_color': '#B24745',
-                                        'line_opacity': 0.5, 'line_width': 2, 'line_curve': 0.1, 
-                                        'line_color': '#9aa7b1', 'repulsion': 500
+                                        'line_opacity': 0.5, 'line_width': 2, 'line_curve': 0, 
+                                        'line_color': '#9aa7b1', 'repulsion': 500, 'font_weight': 'bold'
                                         } 
 
 
@@ -182,12 +182,14 @@ def __init__(self, MainWindow):
         self.actionAny_Table_Mode.setIcon(qta.icon('mdi.table'))
         self.actionCheck_Update.setIcon(qta.icon('mdi.update'))
         self.actionSettings.setIcon(qta.icon('mdi.cog'))
+        self.actionTutorial.setIcon(qta.icon('mdi6.book-open-page-variant-outline'))
         # set menu bar click event
         self.actionTaxaFuncAnalyzer.triggered.connect(self.swith_stack_page_analyzer)
         self.actionPeptide_to_TaxaFunc.triggered.connect(self.swith_stack_page_pep2taxafunc)
         self.actionDatabase_Builder.triggered.connect(self.swith_stack_page_dbuilder)
         self.actionDatabase_Update.triggered.connect(self.swith_stack_page_db_update)
         self.actionAbout.triggered.connect(self.show_about)
+        self.actionTutorial.triggered.connect(self.open_tutorial)
         self.actionRestore_Last_TaxaFunc.triggered.connect(lambda: self.run_restore_taxafunnc_obj_from_file(last=True))
         self.actionRestore_From.triggered.connect(self.run_restore_taxafunnc_obj_from_file)
         self.actionSave_As.triggered.connect(lambda:self.save_metax_obj_to_file(save_path=None, no_message=False))
@@ -1381,7 +1383,15 @@ def check_update(self, show_message=False, manual_check_trigger=True):
         updater = Updater(MetaXGUI=self, version=__version__, splash=splash, show_message=show_message, branch=self.update_branch)
         updater.check_update(show_message=show_message)
 
+    def open_tutorial(self):
+        # use default browser to open the tutorial link
+        from PyQt5.QtGui import QDesktopServices
+        from PyQt5.QtCore import QUrl
 
+        url = QUrl("https://byemaxx.github.io/MetaX/")
+        QDesktopServices.openUrl(url)
+
+
     def show_about(self):
 
         dialog = QDialog(self.MainWindow)
@@ -1406,6 +1416,7 @@ def show_about(self):
         <h3>Aditional Information</h3>
         <p>For more information, please visit:</p>
         <p>GitHub: <a href='https://github.com/byemaxx/MetaX'>The MetaX Project</a></p>
+        <p>Tutorial: <a href='https://byemaxx.github.io/MetaX/' >MetaX Tutorial</a></p>
         <p>iMeta: <a href='https://wiki.imetalab.ca/'>iMetaWiki Page</a></p>
         '''
 
@@ -4836,6 +4847,7 @@ def plot_co_expr_network(self):
                               show_labels=show_labels,
                               rename_taxa=rename_taxa,
                               font_size=font_size,
+                              **self.tf_link_net_params_dict
                               ).plot_co_expression_network(df_type= df_type, corr_method=corr_method, 
                                                                   corr_threshold=corr_threshold, sample_list=sample_list, width=width, height=height, focus_list=focus_list, plot_list_only=plot_list_only)
             self.save_and_show_js_plot(pic, 'co-expression network')

utils/MetaX_GUI/MainWindow.ui

@@ -7382,8 +7382,8 @@
                    <rect>
                     <x>0</x>
                     <y>0</y>
-                    <width>981</width>
-                    <height>332</height>
+                    <width>313</width>
+                    <height>41</height>
                    </rect>
                   </property>
                   <attribute name="label">
@@ -8038,6 +8038,7 @@
     </property>
     <addaction name="actionAbout"/>
     <addaction name="actionCheck_Update"/>
+    <addaction name="actionTutorial"/>
    </widget>
    <widget class="QMenu" name="menuOthers">
     <property name="title">
@@ -8126,6 +8127,11 @@
     <string>Settings</string>
    </property>
   </action>
+  <action name="actionTutorial">
+   <property name="text">
+    <string>Tutorial</string>
+   </property>
+  </action>
  </widget>
  <tabstops>
   <tabstop>comboBox_taxa_level_to_stast</tabstop>

utils/MetaX_GUI/Setting.ui

@@ -24,8 +24,8 @@
        <rect>
         <x>0</x>
         <y>0</y>
-        <width>748</width>
-        <height>367</height>
+        <width>246</width>
+        <height>37</height>
        </rect>
       </property>
       <attribute name="label">
@@ -113,7 +113,7 @@
             <double>0.100000000000000</double>
            </property>
            <property name="value">
-            <double>0.100000000000000</double>
+            <double>0.000000000000000</double>
            </property>
           </widget>
          </item>
@@ -335,7 +335,7 @@
          <item row="2" column="5">
           <widget class="QSpinBox" name="spinBox_tf_link_net_repulsion">
            <property name="maximum">
-            <number>10000</number>
+            <number>100000</number>
            </property>
            <property name="singleStep">
             <number>10</number>
@@ -345,6 +345,37 @@
            </property>
           </widget>
          </item>
+         <item row="3" column="4">
+          <widget class="QLabel" name="label_16">
+           <property name="text">
+            <string>Font Weight</string>
+           </property>
+          </widget>
+         </item>
+         <item row="3" column="5">
+          <widget class="QComboBox" name="comboBox_tf_link_net_font_weight">
+           <item>
+            <property name="text">
+             <string>bold</string>
+            </property>
+           </item>
+           <item>
+            <property name="text">
+             <string>normal</string>
+            </property>
+           </item>
+           <item>
+            <property name="text">
+             <string>bolder</string>
+            </property>
+           </item>
+           <item>
+            <property name="text">
+             <string>lighter</string>
+            </property>
+           </item>
+          </widget>
+         </item>
         </layout>
        </item>
        <item row="0" column="3">

utils/MetaX_GUI/Settings.py

@@ -50,7 +50,7 @@ def __init__(self, parent=None, update_branch="main", auto_check_update=True):
         self.ui.doubleSpinBox_tf_link_net_line_curve.valueChanged.connect(self.handle_tf_link_network_changed)
         self.ui.lineEdit_tf_link_net_line_color.textChanged.connect(self.handle_tf_link_network_changed)
         self.ui.spinBox_tf_link_net_repulsion.valueChanged.connect(self.handle_tf_link_network_changed)
-
+        self.ui.comboBox_tf_link_net_font_weight.currentTextChanged.connect(self.handle_tf_link_network_changed)
 
     def init_ui(self, update_mode, auto_check_update):
         if update_mode == "main":
@@ -88,7 +88,8 @@ def handle_tf_link_network_changed(self):
             "line_curve": self.ui.doubleSpinBox_tf_link_net_line_curve.value(),
             "line_color": self.ui.lineEdit_tf_link_net_line_color.text(),
 
-            'repulsion': self.ui.spinBox_tf_link_net_repulsion.value()
+            'repulsion': self.ui.spinBox_tf_link_net_repulsion.value(),
+            'font_weight': self.ui.comboBox_tf_link_net_font_weight.currentText()
 
         }
         self.tf_link_net_params_dict_changed.emit(network_params_dict)

utils/MetaX_GUI/Ui_MainWindow.py

@@ -3884,7 +3884,7 @@ def setupUi(self, metaX_main):
         self.toolBox_metalab_res_anno = QtWidgets.QToolBox(self.tab_18)
         self.toolBox_metalab_res_anno.setObjectName("toolBox_metalab_res_anno")
         self.page_3 = QtWidgets.QWidget()
-        self.page_3.setGeometry(QtCore.QRect(0, 0, 981, 332))
+        self.page_3.setGeometry(QtCore.QRect(0, 0, 313, 41))
         self.page_3.setObjectName("page_3")
         self.gridLayout_45 = QtWidgets.QGridLayout(self.page_3)
         self.gridLayout_45.setObjectName("gridLayout_45")
@@ -4243,12 +4243,15 @@ def setupUi(self, metaX_main):
         self.actionAny_Table_Mode.setObjectName("actionAny_Table_Mode")
         self.actionSettings = QtWidgets.QAction(metaX_main)
         self.actionSettings.setObjectName("actionSettings")
+        self.actionTutorial = QtWidgets.QAction(metaX_main)
+        self.actionTutorial.setObjectName("actionTutorial")
         self.menuTools.addAction(self.actionTaxaFuncAnalyzer)
         self.menuTools.addAction(self.actionPeptide_to_TaxaFunc)
         self.menuTools.addAction(self.actionDatabase_Builder)
         self.menuTools.addAction(self.actionDatabase_Update)
         self.menuHelp.addAction(self.actionAbout)
         self.menuHelp.addAction(self.actionCheck_Update)
+        self.menuHelp.addAction(self.actionTutorial)
         self.menuOthers.addAction(self.actionRestore_Last_TaxaFunc)
         self.menuOthers.addAction(self.actionRestore_From)
         self.menuOthers.addAction(self.actionSave_As)
@@ -4963,3 +4966,4 @@ def retranslateUi(self, metaX_main):
         self.actionRestore_From.setText(_translate("metaX_main", "Restore From.."))
         self.actionAny_Table_Mode.setText(_translate("metaX_main", "Any Table Mode"))
         self.actionSettings.setText(_translate("metaX_main", "Settings"))
+        self.actionTutorial.setText(_translate("metaX_main", "Tutorial"))

utils/MetaX_GUI/Ui_Setting.py

@@ -20,7 +20,7 @@ def setupUi(self, Settings):
         self.toolBox = QtWidgets.QToolBox(Settings)
         self.toolBox.setObjectName("toolBox")
         self.page = QtWidgets.QWidget()
-        self.page.setGeometry(QtCore.QRect(0, 0, 748, 367))
+        self.page.setGeometry(QtCore.QRect(0, 0, 246, 37))
         self.page.setObjectName("page")
         self.gridLayout_3 = QtWidgets.QGridLayout(self.page)
         self.gridLayout_3.setObjectName("gridLayout_3")
@@ -59,7 +59,7 @@ def setupUi(self, Settings):
         self.doubleSpinBox_tf_link_net_line_curve.setDecimals(1)
         self.doubleSpinBox_tf_link_net_line_curve.setMaximum(1.0)
         self.doubleSpinBox_tf_link_net_line_curve.setSingleStep(0.1)
-        self.doubleSpinBox_tf_link_net_line_curve.setProperty("value", 0.1)
+        self.doubleSpinBox_tf_link_net_line_curve.setProperty("value", 0.0)
         self.doubleSpinBox_tf_link_net_line_curve.setObjectName("doubleSpinBox_tf_link_net_line_curve")
         self.gridLayout_6.addWidget(self.doubleSpinBox_tf_link_net_line_curve, 2, 3, 1, 1)
         self.comboBox_tf_link_net_taxa_sahpe = QtWidgets.QComboBox(self.page_2)
@@ -142,11 +142,21 @@ def setupUi(self, Settings):
         self.label_15.setObjectName("label_15")
         self.gridLayout_6.addWidget(self.label_15, 2, 4, 1, 1)
         self.spinBox_tf_link_net_repulsion = QtWidgets.QSpinBox(self.page_2)
-        self.spinBox_tf_link_net_repulsion.setMaximum(10000)
+        self.spinBox_tf_link_net_repulsion.setMaximum(100000)
         self.spinBox_tf_link_net_repulsion.setSingleStep(10)
         self.spinBox_tf_link_net_repulsion.setProperty("value", 500)
         self.spinBox_tf_link_net_repulsion.setObjectName("spinBox_tf_link_net_repulsion")
         self.gridLayout_6.addWidget(self.spinBox_tf_link_net_repulsion, 2, 5, 1, 1)
+        self.label_16 = QtWidgets.QLabel(self.page_2)
+        self.label_16.setObjectName("label_16")
+        self.gridLayout_6.addWidget(self.label_16, 3, 4, 1, 1)
+        self.comboBox_tf_link_net_font_weight = QtWidgets.QComboBox(self.page_2)
+        self.comboBox_tf_link_net_font_weight.setObjectName("comboBox_tf_link_net_font_weight")
+        self.comboBox_tf_link_net_font_weight.addItem("")
+        self.comboBox_tf_link_net_font_weight.addItem("")
+        self.comboBox_tf_link_net_font_weight.addItem("")
+        self.comboBox_tf_link_net_font_weight.addItem("")
+        self.gridLayout_6.addWidget(self.comboBox_tf_link_net_font_weight, 3, 5, 1, 1)
         self.gridLayout_4.addLayout(self.gridLayout_6, 2, 3, 1, 1)
         self.gridLayout_8 = QtWidgets.QGridLayout()
         self.gridLayout_8.setObjectName("gridLayout_8")
@@ -238,6 +248,11 @@ def retranslateUi(self, Settings):
         self.label_14.setText(_translate("Settings", "Line Curve"))
         self.lineEdit_tf_link_net_line_color.setText(_translate("Settings", "#9aa7b1"))
         self.label_15.setText(_translate("Settings", "Repulsion"))
+        self.label_16.setText(_translate("Settings", "Font Weight"))
+        self.comboBox_tf_link_net_font_weight.setItemText(0, _translate("Settings", "bold"))
+        self.comboBox_tf_link_net_font_weight.setItemText(1, _translate("Settings", "normal"))
+        self.comboBox_tf_link_net_font_weight.setItemText(2, _translate("Settings", "bolder"))
+        self.comboBox_tf_link_net_font_weight.setItemText(3, _translate("Settings", "lighter"))
         self.label_2.setText(_translate("Settings", "Linkage Method"))
         self.comboBox_heatmap_linkage_method.setCurrentText(_translate("Settings", "average"))
         self.comboBox_heatmap_linkage_method.setItemText(0, _translate("Settings", "average"))