Merge branch 'dev'

Docs/ChangeLog.md

@@ -1,3 +1,13 @@
+# Version: 1.119.5
+## Date: 2024-12-3
+### Changes:
+- Fix: add top error when in co-expression part and trends part.
+
+# Version: 1.119.4
+## Date: 2024-12-3
+### Changes:
+- New: added an option to plot violin plot to replace the box plot in the basic plot part.
+
 # Version: 1.119.3
 ## Date: 2024-12-3
 ### Changes:

Docs/MetaX_Cookbook.md

@@ -257,7 +257,7 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
 
   - Select **Sub Meta**  to plot with two meta
 
-    - <img src="MetaX_Cookbook.assets/sub_meta.png" alt="sub_meta"  />
+    - <img src="MetaX_Cookbook.assets/sub_meta.png" >
 
   - Change settings in the **PLOT PARAMETER** tab
 
@@ -269,11 +269,11 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
 
     **e.g. :** Select PBS, BAS and others groups **only in** <u>Individual</u> <u>V1</u> 
 
-    - <img src="MetaX_Cookbook.assets/group_in_condition.png" alt="group_in_condition"  />
+    - <img src="MetaX_Cookbook.assets/group_in_condition.png">
 
   - Select **specific Samples** to Analysis
 
-    - <img src="./MetaX_Cookbook.assets/pca_setting.png" alt="image-20230728113359732"  />
+    - <img src="./MetaX_Cookbook.assets/pca_setting.png" >
 
       
 
@@ -309,7 +309,7 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
 
 ### Heatmap and Bar Plot
 
-<img src="./MetaX_Cookbook.assets/basic_stats_heatmap.png" alt="basic_stats_heatmap"  />
+<img src="./MetaX_Cookbook.assets/basic_stats_heatmap.png" >
 
 - **Select items(Taxa, Function, Taxa-Func and Peptide ) to plot:**
   - Add **All Taxa**, or select one we are interested in.
@@ -340,17 +340,10 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
   - **Rename Samples**: Add group info to each sample name
   - **Rename Taxa**: Only keep the last taxonomic level to reduce to name
   - **Plot Mean**: calculate the mean of each group before plotting
-    
+
   - **Sub Meta:** select a second meta, then combine two meta by mean for Heatmap and 3D bar plot
-    - **<u>For Heatmap</u>**
-      - **Theme**: The theme of the heatmap
-      - **scale**: Scale method of the heatmap
-      - **Show All Labels:** if show all labels in the heatmap
-    - **<u>For Bar</u>**
-      - **Bar Ldg**: Show the legend when plotting Bar
-      - **Bar %:**  Transfer each col to percent when plotting Bar
-      - <img src="./MetaX_Cookbook.assets/basic_stats_heatmap_seeting.png" alt="basic_stats_heatmap_seeting"  />
-
+    - <img src="./MetaX_Cookbook.assets/basic_stats_heatmap_seeting.png" >
+
   - Plot all color maps to view by right click <u>**Theme**</u>
     - ![right_click_theme](MetaX_Cookbook.assets/right_click_theme.png)
     - <img src="MetaX_Cookbook.assets/all_cmap.png" alt="all_cmap">

metax/gui/main_gui.py

@@ -156,7 +156,7 @@ def __init__(self, MainWindow):
         icon_path = os.path.join(os.path.dirname(__file__), "./MetaX_GUI/resources/logo.png")
 
         self.MainWindow.setWindowIcon(QIcon(icon_path))
-        self.MainWindow.resize(1440, 900)
+        self.MainWindow.resize(1200, 800)
         self.MainWindow.setWindowTitle("MetaX v" + __version__)
 
         self.logger = LoggerManager()
@@ -402,7 +402,7 @@ def __init__(self, MainWindow):
         self.comboBox_co_expr_group_sample.currentIndexChanged.connect(lambda:self.change_event_comboBox_group_or_sample('co_expr_group'))
         self.comboBox_trends_group_sample.currentIndexChanged.connect(lambda:self.change_event_comboBox_group_or_sample('trends_group'))
         self.comboBox_tflink_group_sample.currentIndexChanged.connect(lambda:self.change_event_comboBox_group_or_sample('tflink_group'))
-        self.comboBox_radioButton_network_group_sample.currentIndexChanged.connect(lambda:self.change_event_comboBox_group_or_sample('tfnet_group'))
+        self.comboBox_network_group_sample.currentIndexChanged.connect(lambda:self.change_event_comboBox_group_or_sample('tfnet_group'))
 
         ### Peptide Qeruy
         self.pushButton_basic_peptide_query.clicked.connect(self.peptide_query)
@@ -690,7 +690,7 @@ def change_event_comboBox_group_or_sample(self, position):
             'tflink_group': {"current_text": 'comboBox_tflink_group_sample',
                                     "group_layout": ['horizontalLayout_78', 'gridLayout_tflink_group'],
                                     "sample_layout":  ['gridLayout_tflink_sample']},
-            'tfnet_group': {"current_text": 'comboBox_radioButton_network_group_sample',
+            'tfnet_group': {"current_text": 'comboBox_network_group_sample',
                                     "group_layout": ['horizontalLayout_55', 'gridLayout_network_group'],
                                     "sample_layout":  ['gridLayout_network_sample']},
         }
@@ -3640,7 +3640,7 @@ def add_co_expr_top_list(self):
         top_num = self.spinBox_co_expr_top_num.value()
         filtered = self.checkBox_co_expr_top_filtered.isChecked()
         # get sample list
-        if self.radioButton_co_expr_bygroup.isChecked(): # select by group
+        if self.comboBox_co_expr_group_sample.currentText() == 'Group':
             group_list = self.comboBox_co_expr_group.getCheckedItems()
             in_condition = (
                 [self.comboBox_co_expression_condition_meta.currentText(), self.comboBox_co_expression_condition_group.getCheckedItems()]
@@ -3968,7 +3968,6 @@ def add_trends_top_list(self):
         )
 
         # get sample list
-        # if self.radioButton_trends_group.isChecked(): # select by group
         if self.comboBox_trends_group_sample.currentText() == 'Group':
             sample_list = self.get_sample_list_for_group_list_in_condition(group_list, condition=in_condition)
 
@@ -4002,7 +4001,7 @@ def plot_trends_cluster(self):
 
 
         # get sample list and check if the sample list at least has 2 groups
-        if self.radioButton_trends_group.isChecked():
+        if self.comboBox_trends_group_sample.currentText() == 'Group':
             condition = [self.comboBox_trends_condition_meta.currentText(),
                             self.comboBox_trends_condition_group.getCheckedItems()]\
                                 if self.checkBox_trends_in_condition.isChecked() else None
@@ -4121,14 +4120,14 @@ def plot_trends_interactive_line(self):
 
             dft = self.get_table_by_df_type(df_type=table_name, replace_if_two_index = True)
             # get sample list
-            if self.radioButton_trends_group.isChecked():
+            if self.comboBox_trends_group_sample.currentText() == 'Group':
                 group_list = self.comboBox_trends_group.getCheckedItems()
                 group_list = group_list if group_list != [] else sorted(set(self.tfa.group_list))
                 sample_list = self.get_sample_list_for_group_list_in_condition(group_list, condition=condition)
                 if sample_list is None:
                     return None
 
-            else: # self.radioButton_trends_sample.isChecked()
+            else: # select by sample
                 sample_list = self.comboBox_trends_sample.getCheckedItems()
                 if sample_list == []:
                     sample_list = self.tfa.sample_list
@@ -4447,7 +4446,6 @@ def get_title_by_table_name(self, table_name):
         title_name = get_title_by_table_name(self, table_name)
 
         # get sample list when plot by group
-        # if self.radioButton_basic_pca_group.isChecked():
         if self.comboBox_basic_pca_group_sample.currentText() == 'Group':
             condition = [self.comboBox_basic_condition_meta.currentText(), 
                          self.comboBox_basic_condition_group.getCheckedItems()] \
@@ -4499,10 +4497,13 @@ def get_title_by_table_name(self, table_name):
 
             elif method == 'box':
                 plot_samples = self.checkBox_box_plot_samples.isChecked()
+                violinplot = self.checkBox_box_violinplot.isChecked()
+                log_scale = self.checkBox_box_log_scale.isChecked()
                 BasicPlot(self.tfa).plot_box_sns(df=df, title_name=title_name, show_fliers=show_fliers,
                                                  width=width, height=height, font_size=font_size, theme=theme,
                                                  rename_sample = rename_sample, plot_samples = plot_samples, 
-                                                 legend_col_num=legend_col_num, sub_meta = sub_meta)
+                                                 legend_col_num=legend_col_num, sub_meta = sub_meta,
+                                                 violinplot=violinplot, log_scale=log_scale)
 
             elif method == 'corr':
                 cluster = self.checkBox_corr_cluster.isChecked()
@@ -5337,7 +5338,6 @@ def plot_co_expr(self, plot_type = 'network'):
             else:
                 sample_list = slected_list
                 # print(f'Plot with selected samples:{sample_list}')
-        # elif self.radioButton_co_expr_bygroup.isChecked():
         elif self.comboBox_co_expr_group_sample.currentText() == 'Group':
             condition = [self.comboBox_co_expression_condition_meta.currentText(), 
                          self.comboBox_co_expression_condition_group.getCheckedItems()] \
@@ -5520,8 +5520,7 @@ def add_tfnet_top_list(self):
         df_type = self.comboBox_tfnet_table.currentText()
         filtered = self.checkBox_tfnet_top_filtered.isChecked()
 
-        # if self.radioButton_network_bysample.isChecked(): # by sample
-        if self.comboBox_radioButton_network_group_sample.currentText() == 'Sample':
+        if self.comboBox_network_group_sample.currentText() == 'Sample':
             slected_list = self.comboBox_network_sample.getCheckedItems()
             if slected_list:
                 sample_list = slected_list
@@ -5610,7 +5609,7 @@ def plot_network(self):
         rename_taxa = self.checkBox_tf_link_net_rename_taxa.isChecked()
         font_size = self.spinBox_network_font_size.value()
 
-        if self.radioButton_network_bysample.isChecked(): # by sample
+        if self.comboBox_network_group_sample.currentText() == 'Sample':
             slected_list = self.comboBox_network_sample.getCheckedItems()
             if slected_list:
                 sample_list = slected_list
@@ -5656,7 +5655,6 @@ def plot_network(self):
 
     def get_sample_list_tflink(self):
         # get sample list
-        # if self.radioButton_tflink_group.isChecked(): # by group
         if self.comboBox_tflink_group_sample.currentText() == 'Group':
             in_condition = (
                 [self.comboBox_tflink_condition_meta.currentText(), self.comboBox_tflink_condition_group.getCheckedItems()]