New: added an option to plot violin plot to replace the box plot in t…

…he basic plot part. Change: Updated some figures in the cookbook.
byemaxx · Dec 3, 2024 · 7046f89 · 7046f89
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diff --git a/Docs/ChangeLog.md b/Docs/ChangeLog.md
@@ -1,3 +1,8 @@
+# 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:

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/dev_menu.png b/Docs/MetaX_Cookbook.assets/dev_menu.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/group_in_condition.png b/Docs/MetaX_Cookbook.assets/group_in_condition.png
diff --git a/Docs/MetaX_Cookbook.assets/pca_setting.png b/Docs/MetaX_Cookbook.assets/pca_setting.png
diff --git a/Docs/MetaX_Cookbook.assets/settings.png b/Docs/MetaX_Cookbook.assets/settings.png
diff --git a/Docs/MetaX_Cookbook.assets/settings_page2.png b/Docs/MetaX_Cookbook.assets/settings_page2.png
diff --git a/Docs/MetaX_Cookbook.assets/sub_meta.png b/Docs/MetaX_Cookbook.assets/sub_meta.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_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
@@ -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">

diff --git a/metax/gui/main_gui.py b/metax/gui/main_gui.py
@@ -4499,10 +4499,13 @@ 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()