1. Set the HTML plot(e.g. bar, sankey, sunburst, network) as the dark…

… theme when the MetaX theme is dark.

2. Save theme profile to the configuration file when save MetaX_obj.pkl.

Docs/ChangeLog.md

@@ -1,3 +1,8 @@
+# Version: 1.107.4
+## Date: 2024-06-17
+### Changes:
+- Change: Set the HTML plot(e.g. bar, sankey, sunburst, network) as the dark theme when the MetaX theme is dark.
+
 # Version: 1.107.3
 ## Date: 2024-06-16
 ### Changes:

utils/GUI.py

@@ -129,6 +129,9 @@ def __init__(self, MainWindow):
         # Check and load settings
         self.load_basic_Settings()
 
+        # set the default theme mode
+        self.theme = 'white'
+
         #check update
         self.update_required = False
         self.check_update(manual_check_trigger=False)
@@ -163,7 +166,7 @@ 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, 
+                                        'line_opacity': 0.5, 'line_width': 3, 'line_curve': 0, 
                                         'line_color': '#9aa7b1', 'repulsion': 500, 'font_weight': 'bold'
                                         } 
 
@@ -714,6 +717,10 @@ def change_theme(self, theme, silent=False):
             self.show_message(f"Changing theme to {theme}...")
         # save the theme to settings
         self.settings.setValue("theme", theme)
+        # save the theme mode to GUI attribute (dark or light)
+        self.theme = 'dark' if 'dark' in theme else 'white'
+        print(f"Theme mode: {self.theme}")
+
         # recover the .xml suffix
         theme = theme + '.xml'
 
@@ -978,6 +985,10 @@ def save_basic_settings(self, line_edit_name: str | None = None):
         # save update_branch setting
         self.settings.setValue("update_branch", self.update_branch)
         self.settings.setValue("auto_check_update", self.auto_check_update)
+        #save theme
+        if self.settings.contains("theme"):
+            self.settings.setValue("theme", self.settings.value("theme", type=str))
+
 
 
     def save_set_multi_table_settings(self):
@@ -3400,7 +3411,7 @@ def plot_basic_list(self, plot_type='heatmap'):
                     if reply == QMessageBox.No:
                         return None
                 self.show_message(f'Plotting {plot_type}...')
-                pic = BarPlot_js(self.tfa).plot_intensity_bar(df = df, width=width, height=height, 
+                pic = BarPlot_js(self.tfa, theme=self.theme).plot_intensity_bar(df = df, width=width, height=height, 
                                                               title= '', rename_taxa=rename_taxa, 
                                                               show_legend=show_legend, font_size=font_size,
                                                               rename_sample=rename_sample, plot_mean = plot_mean,
@@ -3436,7 +3447,7 @@ def plot_basic_list(self, plot_type='heatmap'):
                 else:
                     title_new = ''
                     subtitle = ''
-                pic = SankeyPlot(self.tfa).plot_intensity_sankey(df=df, width=width, height=height, 
+                pic = SankeyPlot(self.tfa, theme=self.theme).plot_intensity_sankey(df=df, width=width, height=height, 
                                                                  title=title_new, subtitle=subtitle, font_size=font_size,
                                                                  show_legend=self.checkBox_basic_bar_show_legend.isChecked())
                 self.save_and_show_js_plot(pic, title)
@@ -3721,7 +3732,7 @@ def plot_trends_interactive_line(self):
 
 
         try:
-            pic = TrendsPlot_js(self.tfa).plot_trends_js( df=df, width=width, height= height, title=title, 
+            pic = TrendsPlot_js(self.tfa, theme=self.theme).plot_trends_js( df=df, width=width, height= height, title=title, 
                                                          rename_taxa=rename_taxa, show_legend=show_legend, 
                                                          add_group_name = plot_samples, font_size=font_size)
             self.save_and_show_js_plot(pic, f'Cluster {cluster_num+1} of {table_name}')
@@ -3796,7 +3807,7 @@ def save_and_show_js_plot(self, pic, title, width=None, height=None):
             pic.render(save_path)
             self.logger.write_log(f'html saved: {save_path}', 'i')
 
-            web = webDialog.MyDialog(save_path, None)
+            web = webDialog.WebDialog(save_path, None, theme=self.theme)
             if title:
                 web.setWindowTitle(title)
 
@@ -4039,7 +4050,9 @@ def get_title_by_table_name(self, table_name):
                     QMessageBox.warning(self.MainWindow, 'Warning', 'The number of rows is less than 3, PCA 3D cannot be plotted!')
                     return None
                 self.show_message('PCA is running, please wait...')
-                pic = PcaPlot_js(self.tfa).plot_pca_pyecharts_3d(df=df, title_name=title_name, show_label = show_label, 
+                pic = PcaPlot_js(self.tfa,
+                                 theme=self.theme
+                                 ).plot_pca_pyecharts_3d(df=df, title_name=title_name, show_label = show_label, 
                                                                  rename_sample = rename_sample,
                                                                 width=width, height=height, font_size=font_size, legend_col_num=legend_col_num)
                 self.save_and_show_js_plot(pic, f'PCA 3D of {title_name}')
@@ -4096,7 +4109,7 @@ def get_title_by_table_name(self, table_name):
                 else:
                     show_label = False
 
-                pic = SunburstPlot().create_sunburst_chart(taxa_df= taxa_df, width=width, height=height,
+                pic = SunburstPlot(theme=self.theme).create_sunburst_chart(taxa_df= taxa_df, width=width, height=height,
                                                         title='Sunburst of Taxa', show_label=show_label,
                                                         label_font_size = font_size)
                 self.save_and_show_js_plot(pic, 'Sunburst of Taxa')
@@ -4108,7 +4121,7 @@ def get_title_by_table_name(self, table_name):
 
                 taxa_df = self.tfa.taxa_df[sample_list]
 
-                pic = TreeMapPlot().create_treemap_chart(taxa_df= taxa_df, width=width, height=height,
+                pic = TreeMapPlot(theme=self.theme).create_treemap_chart(taxa_df= taxa_df, width=width, height=height,
                                                         show_sub_title = self.checkBox_pca_if_show_lable.isChecked(),
                                                         font_size = font_size)
                 self.save_and_show_js_plot(pic, 'Treemap of Taxa')
@@ -4122,7 +4135,7 @@ def get_title_by_table_name(self, table_name):
                 df = df[sample_list]
                 title = 'Sankey of Taxa' if table_name == 'Taxa' else 'Sankey of Taxa-Functions'
 
-                pic = SankeyPlot(self.tfa).plot_intensity_sankey(df=df, width=width, height=height,
+                pic = SankeyPlot(self.tfa, theme=self.theme).plot_intensity_sankey(df=df, width=width, height=height,
                                                                  font_size = font_size, title='', subtitle='')
                 self.save_and_show_js_plot(pic, title)
 
@@ -4791,7 +4804,7 @@ def plot_deseq2_volcano(self):
         # VolcanoPlot().plot_volcano(df, padj = pvalue, log2fc = log2fc,  title_name='2 groups',  width=width, height=height)
         try:
             df = self.table_dict[table_name]
-            pic = VolcanoPlot().plot_volcano_js(df, pvalue = pvalue, p_type = p_type,
+            pic = VolcanoPlot(theme=self.theme).plot_volcano_js(df, pvalue = pvalue, p_type = p_type,
                                                 log2fc_min = log2fc_min, log2fc_max=log2fc_max, 
                                                 title_name=title_name,  font_size = font_size,
                                                 width=width, height=height)
@@ -4844,6 +4857,7 @@ def plot_co_expr_network(self):
                               show_labels=show_labels,
                               rename_taxa=rename_taxa,
                               font_size=font_size,
+                              theme=self.theme,
                               **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)
@@ -4890,7 +4904,7 @@ def deseq2_plot_sankey(self):
             df = self.table_dict[table_name]
             title_name = f'{group1} vs {group2} of {table_name.split("(")[1].split(")")[0]}'
 
-            pic = SankeyPlot(self.tfa).plot_fc_sankey(df, width=width, height=height, pvalue=pvalue, p_type = p_type,
+            pic = SankeyPlot(self.tfa, theme=self.theme).plot_fc_sankey(df, width=width, height=height, pvalue=pvalue, p_type = p_type,
                                                       log2fc_min=log2fc_min, log2fc_max=log2fc_max, title =title_name, font_size=font_size)
             self.save_and_show_js_plot(pic, f'Sankay plot {title_name}')
 
@@ -5072,6 +5086,7 @@ def plot_network(self):
                               show_labels=show_labels,
                               rename_taxa=rename_taxa,
                               font_size=font_size,
+                              theme=self.theme,
                             **self.tf_link_net_params_dict
                               ).plot_tflink_network(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, 'taxa-func link Network')
@@ -5340,7 +5355,7 @@ def plot_tflink_bar(self):
             params['show_all_labels'] = show_all_labels
 
             self.show_message('Plotting bar plot, please wait...')
-            pic = BarPlot_js(self.tfa).plot_intensity_bar(**params)
+            pic = BarPlot_js(self.tfa, theme=self.theme).plot_intensity_bar(**params)
             self.save_and_show_js_plot(pic, 'Intensity Bar Plot')
 
 

utils/MetaX_GUI/MainWindow.ui

@@ -46,7 +46,7 @@
            <enum>Qt::LeftToRight</enum>
           </property>
           <property name="currentIndex">
-           <number>5</number>
+           <number>6</number>
           </property>
           <widget class="QWidget" name="tab">
            <attribute name="title">
@@ -240,7 +240,7 @@
                  <x>0</x>
                  <y>0</y>
                  <width>496</width>
-                 <height>373</height>
+                 <height>377</height>
                 </rect>
                </property>
                <attribute name="label">
@@ -5301,6 +5301,9 @@
                       <property name="text">
                        <string>Rename Taxa</string>
                       </property>
+                      <property name="checked">
+                       <bool>true</bool>
+                      </property>
                      </widget>
                     </item>
                    </layout>
@@ -7081,6 +7084,9 @@
                     <property name="text">
                      <string>Raname Taxa</string>
                     </property>
+                    <property name="checked">
+                     <bool>true</bool>
+                    </property>
                    </widget>
                   </item>
                  </layout>
@@ -8020,7 +8026,7 @@
      <x>0</x>
      <y>0</y>
      <width>1059</width>
-     <height>23</height>
+     <height>21</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuTools">
@@ -8546,37 +8552,5 @@
     </hint>
    </hints>
   </connection>
-  <connection>
-   <sender>checkBox_co_expr_show_label</sender>
-   <signal>clicked(bool)</signal>
-   <receiver>spinBox_co_expr_font_size</receiver>
-   <slot>setEnabled(bool)</slot>
-   <hints>
-    <hint type="sourcelabel">
-     <x>917</x>
-     <y>336</y>
-    </hint>
-    <hint type="destinationlabel">
-     <x>1012</x>
-     <y>313</y>
-    </hint>
-   </hints>
-  </connection>
-  <connection>
-   <sender>checkBox_tf_link_net_show_label</sender>
-   <signal>clicked(bool)</signal>
-   <receiver>spinBox_network_font_size</receiver>
-   <slot>setEnabled(bool)</slot>
-   <hints>
-    <hint type="sourcelabel">
-     <x>203</x>
-     <y>123</y>
-    </hint>
-    <hint type="destinationlabel">
-     <x>203</x>
-     <y>127</y>
-    </hint>
-   </hints>
-  </connection>
  </connections>
 </ui>

utils/MetaX_GUI/Setting.ui

@@ -314,7 +314,7 @@
             <double>1.000000000000000</double>
            </property>
            <property name="value">
-            <double>2.000000000000000</double>
+            <double>3.000000000000000</double>
            </property>
           </widget>
          </item>

utils/MetaX_GUI/Ui_MainWindow.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\utils\MetaX_GUI\MainWindow.ui'
+# Form implementation generated from reading ui file 'c:\Users\Qing\OneDrive - University of Ottawa\code\TaxaFunc\MetaX\utils\MetaX_GUI\MainWindow.ui'
 #
 # Created by: PyQt5 UI code generator 5.15.9
 #
@@ -145,7 +145,7 @@ 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, 496, 373))
+        self.page_2.setGeometry(QtCore.QRect(0, 0, 496, 377))
         self.page_2.setObjectName("page_2")
         self.gridLayout_27 = QtWidgets.QGridLayout(self.page_2)
         self.gridLayout_27.setObjectName("gridLayout_27")
@@ -2779,6 +2779,7 @@ def setupUi(self, metaX_main):
         self.formLayout.setWidget(3, QtWidgets.QFormLayout.LabelRole, self.checkBox_co_expr_show_label)
         self.checkBox_co_expr_rename_taxa = QtWidgets.QCheckBox(self.tab_5)
         self.checkBox_co_expr_rename_taxa.setEnabled(True)
+        self.checkBox_co_expr_rename_taxa.setChecked(True)
         self.checkBox_co_expr_rename_taxa.setObjectName("checkBox_co_expr_rename_taxa")
         self.formLayout.setWidget(3, QtWidgets.QFormLayout.FieldRole, self.checkBox_co_expr_rename_taxa)
         self.verticalLayout_3.addLayout(self.formLayout)
@@ -3721,6 +3722,7 @@ def setupUi(self, metaX_main):
         self.horizontalLayout_57.addWidget(self.checkBox_tf_link_net_show_label)
         self.checkBox_tf_link_net_rename_taxa = QtWidgets.QCheckBox(self.tab_9)
         self.checkBox_tf_link_net_rename_taxa.setEnabled(True)
+        self.checkBox_tf_link_net_rename_taxa.setChecked(True)
         self.checkBox_tf_link_net_rename_taxa.setObjectName("checkBox_tf_link_net_rename_taxa")
         self.horizontalLayout_57.addWidget(self.checkBox_tf_link_net_rename_taxa)
         self.gridLayout_6.addLayout(self.horizontalLayout_57, 10, 3, 1, 1)
@@ -4206,7 +4208,7 @@ 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, 1059, 23))
+        self.menuBar.setGeometry(QtCore.QRect(0, 0, 1059, 21))
         self.menuBar.setObjectName("menuBar")
         self.menuTools = QtWidgets.QMenu(self.menuBar)
         self.menuTools.setObjectName("menuTools")
@@ -4266,7 +4268,7 @@ def setupUi(self, metaX_main):
 
         self.retranslateUi(metaX_main)
         self.stackedWidget.setCurrentIndex(0)
-        self.tabWidget_TaxaFuncAnalyzer.setCurrentIndex(5)
+        self.tabWidget_TaxaFuncAnalyzer.setCurrentIndex(6)
         self.toolBox_2.setCurrentIndex(0)
         self.tabWidget_4.setCurrentIndex(1)
         self.tabWidget_3.setCurrentIndex(0)
@@ -4300,8 +4302,6 @@ def setupUi(self, metaX_main):
         self.checkBox_pca_if_show_lable.clicked['bool'].connect(self.checkBox_pca_if_adjust_pca_label.setEnabled) # type: ignore
         self.checkBox_pca_if_show_lable.clicked['bool'].connect(self.checkBox_sunburst_show_all_lables.setEnabled) # type: ignore
         self.checkBox_pca_if_show_lable.clicked['bool'].connect(self.doubleSpinBox_basic_pca_label_font_transparency.setEnabled) # type: ignore
-        self.checkBox_co_expr_show_label.clicked['bool'].connect(self.spinBox_co_expr_font_size.setEnabled) # type: ignore
-        self.checkBox_tf_link_net_show_label.clicked['bool'].connect(self.spinBox_network_font_size.setEnabled) # type: ignore
         QtCore.QMetaObject.connectSlotsByName(metaX_main)
         metaX_main.setTabOrder(self.comboBox_taxa_level_to_stast, self.toolButton_meta_table_help)
         metaX_main.setTabOrder(self.toolButton_meta_table_help, self.comboBox_function_to_stast)

utils/MetaX_GUI/Ui_Setting.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\utils\MetaX_GUI\Setting.ui'
+# Form implementation generated from reading ui file 'c:\Users\Qing\OneDrive - University of Ottawa\code\TaxaFunc\MetaX\utils\MetaX_GUI\Setting.ui'
 #
 # Created by: PyQt5 UI code generator 5.15.9
 #
@@ -132,7 +132,7 @@ def setupUi(self, Settings):
         self.doubleSpinBox_tf_link_net_line_width.setDecimals(1)
         self.doubleSpinBox_tf_link_net_line_width.setMinimum(0.1)
         self.doubleSpinBox_tf_link_net_line_width.setSingleStep(1.0)
-        self.doubleSpinBox_tf_link_net_line_width.setProperty("value", 2.0)
+        self.doubleSpinBox_tf_link_net_line_width.setProperty("value", 3.0)
         self.doubleSpinBox_tf_link_net_line_width.setObjectName("doubleSpinBox_tf_link_net_line_width")
         self.gridLayout_6.addWidget(self.doubleSpinBox_tf_link_net_line_width, 2, 1, 1, 1)
         self.lineEdit_tf_link_net_line_color = QtWidgets.QLineEdit(self.page_2)

utils/MetaX_GUI/webDialog.py

@@ -7,9 +7,9 @@
 import os
 from PyQt5.QtWidgets import QApplication
 
-class MyDialog(QDialog):
-    def __init__(self, html_path=None, parent=None):
-        super(MyDialog, self).__init__(parent)
+class WebDialog(QDialog):
+    def __init__(self, html_path=None, parent=None, theme="white"):
+        super(WebDialog, self).__init__(parent)
         self.setWindowTitle('HTML Viewer')
         self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
         self.resize(1800, 1000)
@@ -21,13 +21,14 @@ def __init__(self, html_path=None, parent=None):
         self.exportButton.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Fixed)
         self.webEngineView = QWebEngineView(self)
         self.html_path = html_path
-
+
+        self.init_background_color(theme)
 
         layout = QVBoxLayout(self)
         layout.addWidget(self.exportButton)
-        layout2 = QHBoxLayout()  # 创建一个水平布局
+        layout2 = QHBoxLayout()
 
-        layout.addLayout(layout2)  # 将水平布局添加到垂直布局中
+        layout.addLayout(layout2)
         layout.addWidget(self.webEngineView)
 
         self.exportButton.clicked.connect(self.export_html)
@@ -42,6 +43,12 @@ def __init__(self, html_path=None, parent=None):
             icon_path = os.path.join(os.path.dirname(__file__), "./resources/logo.png")
             self.setWindowIcon(QIcon(icon_path))
 
+    def init_background_color(self, theme_mode):
+        if theme_mode == "dark":
+            # set background color to #100c2a
+            from PyQt5.QtGui import QColor
+            self.webEngineView.page().setBackgroundColor(QColor("#100c2a"))
+
     def zoom(self, value):
         self.webEngineView.setZoomFactor(value / 100) 
 
@@ -74,6 +81,6 @@ def export_html(self):
 
 if __name__ == '__main__':
     app = QApplication(sys.argv)
-    dialog = MyDialog(html_path="./sankey.html")
+    dialog = WebDialog(html_path="C:/Users/Qing/MetaX/html/Bar_of_Functions.html", theme="dark")
     dialog.show()
     sys.exit(app.exec_())