1. Added more options for the Taxa-Functions Network plot, including …

…the color, label, layout, and edge width. etc.

2. Updated the MetaX_Cookbook.md and README.md to reflect the changes.

Docs/ChangeLog.md

@@ -1,3 +1,8 @@
+# Version: 1.107.1
+## Date: 2024-06-16
+### Changes:
+- New: Added more options for the Taxa-Functions Network plot, including the color, label, layout, and edge width. etc.
+
 # Version: 1.107.0
 ## Date: 2024-06-15
 ### Changes:

Docs/MetaX_Cookbook.md

@@ -35,12 +35,16 @@ Visit **Github** to get more information:
 
 # Module 1. Database Builder
 
+**NOTE:** the result of **<u>MetaLab v2.3</u>** MaxQuant workflow do not need Build Database. However, we do not recommend the result files from this version of MetaLab as input to MetaX, and large amounts of Peptide may be discarded.
+
+
+
 - You have to build the database for **the first time** using <u>Database Builder</u>.
 
   **(Option 1) Build Database By MGnify Data**
-  
+
   Make sure to download the correct database type corresponding to your data
-  
+
 
 
 <img src="./MetaX_Cookbook.assets/dbbuilder.png" alt="dbbuilder"  />
@@ -115,6 +119,10 @@ Visit **Github** to get more information:
 
 # Module 3. Peptide Annotator
 
+## 1. Result From MAG:
+
+The peptide result form Metagenome-assembled *genomes* (*MAGs*) as the reference database for proteins search, e.g. MetaLab-MAG, and other database like  MGnify.
+
 - Annotate the peptide to TaxaFunc before analyzing by <u>**Peptide Annotator**</u>
 
   <img src="./MetaX_Cookbook.assets/peptide2taxafunc.png" alt="peptide2taxafunc"  />
@@ -143,7 +151,20 @@ Visit **Github** to get more information:
 
     <img src="./MetaX_Cookbook.assets/LCA_prop.png" alt="LCA_prop" style="zoom:50%;" />
 
+## 2. Results from MetaLab 2.3:
+
+The peptide result from **<u>MetaLab 2.3</u>** MaxQuant workflow
+
+- Select the **MetaLab** result folder, which contains the **maxquant_search** folder.
+
+  - ![peptide2taxafunc_tab2_1](MetaX_Cookbook.assets\peptide2taxafunc_tab2_1.png)
 
+- Then the **Peptide Annotator** will automatically find the **peptides_report.txt**, **BuiltIn.pepTaxa.csv** and **functions.tsv** in the **maxquant_search** folder. Or you can select the files manually.
+
+
+
+  - Select the **OTFs Save To** to set the location to save the result table.
+  - ![peptide2taxafunc_tab2_2](MetaX_Cookbook.assets\peptide2taxafunc_tab2_2.png)
 
 
 # Module 4. OTF Analyzer
@@ -683,26 +704,27 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
 
   <img src="./MetaX_Cookbook.assets/bar_to_line.png" alt="bar_to_line"  />
 
-  ### Taxa-Func Network
-
-  - Select some groups or samples (default all)
-  - add some taxa, func or taxa-func to focus the window  (Optional)
-
-  <img src="./MetaX_Cookbook.assets/taxa_func_link_page.png" alt="image-20230728145518517"  />
-
-  - Plot list only
-    - Checked the "**Plot List Only**" to show the items only in the list
-
-  - Network plot
-    - The yellow dots are taxa, and the grey dots are functions, the size of the dots presents the intensity
-    - The red dots are the taxa we focused on
-    - The green dots are the functions we focused on
-
-  <img src="./MetaX_Cookbook.assets/taxa_func_network.png" alt="taxa_func_network"  />
-
-
 
-# Restore Last TaxaFunc Object
+### Taxa-Func Network
+
+- Select some groups or samples (default all)
+- add some taxa, func or taxa-func to focus the window  (Optional)
+
+<img src="./MetaX_Cookbook.assets/taxa_func_link_page.png" alt="image-20230728145518517"  />
+
+- Plot list only
+  - Checked the "**Plot List Only**" to show the items only in the list
+
+- Network plot
+  - The yellow dots are taxa, and the grey dots are functions, the size of the dots presents the intensity
+  - The red dots are the taxa we focused on
+  - The green dots are the functions we focused on
+
+<img src="./MetaX_Cookbook.assets/taxa_func_network.png" alt="taxa_func_network"  />
+
+
+
+## 8. Restore Last TaxaFunc Object
 
 - Once you create TaxaFunc, the <u>TaxaFunc Object</u> will save automatically, and you can restore it next time.
 - Also, we can export the current MetaX to a file and reload it again.
@@ -733,7 +755,9 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
   - Check the box of **Auto Check Update** to enable or disable check update when launching
   - Change to update from the **stable version** or **beta version** by settings
   - <img src="MetaX_Cookbook.assets/settings.png" alt="settings"  />
-
+  - Other Options Settings
+  - ![settings_page2](C:\Users\max\OneDrive - University of Ottawa\code\TaxaFunc\MetaX\docs\MetaX_Cookbook.assets\settings_page2.png)
+
 
 
 

README.md

@@ -7,7 +7,9 @@ MetaX also features <u>statistical modules</u> and <u>plotting tools</u> for ana
 
 ![abstract](./Docs/MetaX_Cookbook.assets/abstract.png)
 ## 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)
 
 ## Download
 ### `Desktop Version(Recommended)`:

utils/GUI.py

@@ -160,6 +160,13 @@ def __init__(self, MainWindow):
         # ploting parameters
         self.heatmap_params_dict = {'linkage_method': 'average', 'distance_metric': 'euclidean'}
 
+        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
+                                        } 
+
 
         # set icon
         self.actionTaxaFuncAnalyzer.setIcon(qta.icon('mdi.chart-areaspline'))
@@ -632,15 +639,19 @@ def show_settings_window(self):
             self.settings_dialog.setWindowTitle("Settings")
             self.settings_dialog.setModal(False) 
             layout = QVBoxLayout(self.settings_dialog)
-            self.settings_dialog.resize(600, 400)
+            self.settings_dialog.resize(900, 600)
 
             settings_widget = SettingsWidget(self.settings_dialog, self.update_branch, self.auto_check_update)
             settings_widget.update_mode_changed.connect(self.on_update_mode_changed)
             settings_widget.auto_check_update_changed.connect(self.on_auto_check_update_changed)
             settings_widget.heatmap_params_dict_changed.connect(self.on_heatmap_params_changed)
+            settings_widget.tf_link_net_params_dict_changed.connect(self.on_tf_link_net_params_changed)
 
             layout.addWidget(settings_widget)
             self.settings_dialog.setLayout(layout)
+
+            # set not pin to top
+            self.settings_dialog.setWindowFlags(self.settings_dialog.windowFlags() & ~Qt.WindowStaysOnTopHint)
 
         self.settings_dialog.show()
 
@@ -659,6 +670,10 @@ def on_auto_check_update_changed(self, auto_check):
     def on_heatmap_params_changed(self, params_dict):
         self.heatmap_params_dict = params_dict
         print(f"Heatmap params changed to: {params_dict}")
+
+    def on_tf_link_net_params_changed(self, params_dict):
+        self.tf_link_net_params_dict = params_dict
+        print(f"Taxa-func link network params changed to: {params_dict}")
 
     ###############   basic function End   ###############
 
@@ -4790,8 +4805,10 @@ def plot_co_expr_network(self):
         height = self.spinBox_co_expr_height.value()
         focus_list = self.co_expr_focus_list
         plot_list_only = self.checkBox_co_expr_plot_list_only.isChecked()
-
-
+        show_labels = self.checkBox_co_expr_show_label.isChecked()
+        rename_taxa = self.checkBox_co_expr_rename_taxa.isChecked()
+        font_size = self.spinBox_co_expr_font_size.value()
+
         sample_list = self.tfa.sample_list
         if self.radioButton_co_expr_bysample.isChecked():
             slected_list = self.comboBox_co_expr_sample.getCheckedItems()
@@ -4813,9 +4830,13 @@ def plot_co_expr_network(self):
                 return None
 
 
-        try:
+        try:            
             self.show_message('Co-expression network is plotting...\n\n It may take a long time! Please wait...')
-            pic = NetworkPlot(self.tfa).plot_co_expression_network(df_type= df_type, corr_method=corr_method, 
+            pic = NetworkPlot(self.tfa,
+                              show_labels=show_labels,
+                              rename_taxa=rename_taxa,
+                              font_size=font_size,
+                              ).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')
         except ValueError as e:
@@ -5020,6 +5041,10 @@ def plot_network(self):
         sample_list =  self.tfa.sample_list
         focus_list = self.tfnet_fcous_list
         plot_list_only = self.checkBox_tf_link_net_plot_list_only.isChecked()
+        show_labels = self.checkBox_tf_link_net_show_label.isChecked()
+        rename_taxa = self.checkBox_tf_link_net_rename_taxa.isChecked()
+        font_size = self.spinBox_network_font_size.value()
+
 
         if self.radioButton_network_bysample.isChecked():
             slected_list = self.comboBox_network_sample.getCheckedItems()
@@ -5034,7 +5059,12 @@ def plot_network(self):
             # print(f'Plot with selected groups:{groups} and samples:{sample_list}')
         try:
             self.show_message('Plotting network...')
-            pic = NetworkPlot(self.tfa).plot_tflink_network(sample_list=sample_list, width=width, height=height, focus_list=focus_list,plot_list_only=plot_list_only)
+            pic = NetworkPlot(self.tfa,
+                              show_labels=show_labels,
+                              rename_taxa=rename_taxa,
+                              font_size=font_size,
+                            **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')
         except Exception as e:
             error_message = traceback.format_exc()