Merge branch 'dev'

byemaxx · Jul 24, 2024 · 2171364 · 2171364
2 parents 195b9a4 + 3595ac6
commit 2171364
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diff --git a/Docs/ChangeLog.md b/Docs/ChangeLog.md
@@ -1,3 +1,9 @@
+# Version: 1.109.3
+## Date: 2024-07-24
+### Changes:
+- Change: Optimized the UI of plot settings.
+
+
 # Version: 1.109.2
 ## Date: 2024-07-23
 ### Changes:

diff --git a/Docs/MetaX_Cookbook.assets/anova_test.png b/Docs/MetaX_Cookbook.assets/anova_test.png
diff --git a/Docs/MetaX_Cookbook.assets/basic_setting.png b/Docs/MetaX_Cookbook.assets/basic_setting.png
diff --git a/Docs/MetaX_Cookbook.assets/basic_stats_heatmap.png b/Docs/MetaX_Cookbook.assets/basic_stats_heatmap.png
diff --git a/Docs/MetaX_Cookbook.assets/basic_stats_heatmap_seeting.png b/Docs/MetaX_Cookbook.assets/basic_stats_heatmap_seeting.png
diff --git a/Docs/MetaX_Cookbook.assets/basic_stats_pca.png b/Docs/MetaX_Cookbook.assets/basic_stats_pca.png
diff --git a/Docs/MetaX_Cookbook.assets/co_network_page.png b/Docs/MetaX_Cookbook.assets/co_network_page.png
diff --git a/Docs/MetaX_Cookbook.assets/co_network_setting.png b/Docs/MetaX_Cookbook.assets/co_network_setting.png
diff --git a/Docs/MetaX_Cookbook.assets/deseq2.png b/Docs/MetaX_Cookbook.assets/deseq2.png
diff --git a/Docs/MetaX_Cookbook.assets/group_control_test.png b/Docs/MetaX_Cookbook.assets/group_control_test.png
diff --git a/Docs/MetaX_Cookbook.assets/t_test.png b/Docs/MetaX_Cookbook.assets/t_test.png
diff --git a/Docs/MetaX_Cookbook.assets/taxa_func_link_net_settings.png b/Docs/MetaX_Cookbook.assets/taxa_func_link_net_settings.png
diff --git a/Docs/MetaX_Cookbook.assets/taxa_func_link_page.png b/Docs/MetaX_Cookbook.assets/taxa_func_link_page.png
diff --git a/Docs/MetaX_Cookbook.assets/taxa_func_link_page2.png b/Docs/MetaX_Cookbook.assets/taxa_func_link_page2.png
diff --git a/Docs/MetaX_Cookbook.assets/trends_page.png b/Docs/MetaX_Cookbook.assets/trends_page.png
diff --git a/Docs/MetaX_Cookbook.md b/Docs/MetaX_Cookbook.md
@@ -350,7 +350,7 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
 
   - Change settings in the **PLOT PARAMETER** tab
 
-    - <img src="MetaX_Cookbook.assets/basic_setting.png" alt="basic_setting" style="zoom:80%;" />
+    - <img src="MetaX_Cookbook.assets/basic_setting.png" alt="basic_setting"  />
 
       
 
@@ -565,7 +565,7 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
 
 
 
-<img src="./MetaX_Cookbook.assets/deseq2.png" alt="image-20230728123725717"/>
+<img src="./MetaX_Cookbook.assets/deseq2.png">
 
 - Select <u>p-adjust</u>, <u>log2FC</u> to plot
 

diff --git a/metax/gui/main_gui.py b/metax/gui/main_gui.py
@@ -43,7 +43,7 @@
 from PyQt5.QtWidgets import QDialog, QVBoxLayout, QTextBrowser
 from PyQt5.QtGui import QIcon
 from PyQt5.QtCore import Qt, QTimer, QDir, QSettings
-from PyQt5.QtWidgets import QToolBox
+from PyQt5.QtWidgets import QToolBox, QGroupBox
 
 import qtawesome as qta
 # from qt_material import apply_stylesheet
@@ -398,9 +398,6 @@ def __init__(self, MainWindow):
 
         ### ANOVA
         self.pushButton_anova_test.clicked.connect(self.anova_test)
-
-        ### Group Control Test
-        self.hide_all_in_layout(self.gridLayout_38)
 
         # self.hiddenTab = self.tabWidget_3.widget(3)
         # self.tabWidget_3.removeTab(3)
@@ -512,6 +509,9 @@ def __init__(self, MainWindow):
         self.toolButton_db_anno_folder_help.clicked.connect(self.show_toolButton_db_anno_folder_help)
 
         self.set_change_event_for_all_condition_group()
+
+        # hide ploting setting groupbox
+        self.hide_plot_setting_groupbox()
 
         # init theme
         self.init_theme_menu()
@@ -768,6 +768,17 @@ def change_event_comboBox_3dbar_sub_meta(self):
         # else:
         #     self.comboBox_3dbar_sub_meta.setEnabled(True)
 
+    def hide_plot_setting_groupbox(self):
+        groupbox_list = ["groupBox_basic_plot", "groupBox_basic_heatmap_plot_settings", 
+                         "groupBox_cross_heatmap_settings", "groupBox_deseq2_plot_settings",
+                         "groupBox_co_expression_plot_settings", "groupBox_expression_trends_plot_settings",
+                         "groupBox_taxa_func_link_plot_settings", "groupBox_taxa_func_link_net_plot_settings"
+                         ]
+        for groupbox_name in groupbox_list:
+            groupbox = getattr(self, groupbox_name)
+            groupbox.setVisible(False)
+
+
 
     ###############   basic function End   ###############
 
@@ -1442,56 +1453,14 @@ def swith_stack_page_dbuilder(self):
     def swith_stack_page_db_update(self):
         self.stackedWidget.setCurrentIndex(3)
 
-    # def swith_stack_page_about(self):
-    #     self.stackedWidget.setCurrentIndex(3)
 
     def cross_test_tab_change(self, index):        
         if index in [3, 4]: # TUKEY Test or DESeq2 Test
-            # self.hide_all_in_layout(self.gridLayout_top_heatmap_plot)
-            self.hide_all_in_layout(self.toolBox_9)
-        else:
-            self.show_all_in_layout(self.toolBox_9)
-
-        if index == 2: # Group Control Test
-            self.hide_all_in_layout(self.gridLayout_38)
+            self.groupBox_cross_heatmap_plot.setVisible(False)
         else:
-            self.show_all_in_layout(self.gridLayout_38)
+            self.groupBox_cross_heatmap_plot.setVisible(True)
 
 
-
-    def hide_all_in_layout(self, layout):
-        if isinstance(layout, QToolBox):
-            # For QToolBox
-            layout.hide()
-        else:
-            # For other types of layout
-            for i in range(layout.count()):
-                layout_item = layout.itemAt(i)
-                if layout_item.widget() is not None:
-                    layout_item.widget().hide()
-                elif layout_item.layout() is not None:
-                    self.hide_all_in_layout(layout_item.layout())
-
-    def show_all_in_layout(self, layout, if_except=True):
-        except_list = ['doubleSpinBox_mini_log2fc_heatmap', 'label_138',
-                    'comboBox_cross_3_level_plot_df_type', 'label_141',
-                    'checkBox_cross_3_level_plot_remove_zero_col', 'label_139',
-                    'doubleSpinBox_max_log2fc_heatmap'] if if_except else []
-
-        if isinstance(layout, QToolBox):
-            # For QToolBox
-            layout.show()
-        else:
-            # For other types of layout
-            for i in range(layout.count()):
-                layout_item = layout.itemAt(i)
-                if layout_item.widget() is not None:
-                    if layout_item.widget().objectName() not in except_list:
-                        layout_item.widget().show()
-                elif layout_item.layout() is not None:
-                    self.show_all_in_layout(layout_item.layout(), if_except=if_except)
-
-
     def add_theme_to_combobox(self):
         # get all themes
         from matplotlib import colormaps
@@ -2275,7 +2244,6 @@ def change_event_comboBox_top_heatmap_table(self):
 
             if 'dunnett_test' in selected_table_name:
                 self.comboBox_top_heatmap_sort_type.setEnabled(False)      
-                self.hide_all_in_layout(self.gridLayout_38)
 
             if selected_table_name.startswith('deseq2allin') or selected_table_name.startswith('dunnettAllCondtion'):
                 self.comboBox_cross_3_level_plot_df_type.setEnabled(True)
@@ -2284,7 +2252,6 @@ def change_event_comboBox_top_heatmap_table(self):
 
             if selected_table_name.startswith('deseq2'):
 
-                self.show_all_in_layout(self.gridLayout_38, if_except=False)
                 self.doubleSpinBox_mini_log2fc_heatmap.setEnabled(True)
                 self.doubleSpinBox_max_log2fc_heatmap.setEnabled(True)
 
@@ -2299,14 +2266,12 @@ def change_event_comboBox_top_heatmap_table(self):
                     self.comboBox_top_heatmap_sort_type.addItems(['padj', 'pvalue'])
 
             if selected_table_name.startswith('dunnettAllCondtion'):
-                self.show_all_in_layout(self.gridLayout_38, if_except=False)
                 self.doubleSpinBox_mini_log2fc_heatmap.setEnabled(False)
                 self.doubleSpinBox_max_log2fc_heatmap.setEnabled(False)
                 self.comboBox_top_heatmap_sort_type.setEnabled(False)
 
 
         else:
-            self.hide_all_in_layout(self.gridLayout_38)
             self.label_57.setText('Sort By:')
             sort_type_list =  ["p-value", "f-statistic (ANOVA)", "t-statistic (T-Test)"]
             if 't_test' in selected_table_name: