Merge branch 'dev'

Docs/MetaX_Cookbook.md

@@ -608,15 +608,15 @@ We can select <u>**meta**</u> <u>**groups**</u> or <u>**samples**</u> (default a
 
   - Select some groups (Default all) to get **the intensity of each taxon of this function**
 
-    <img src="./MetaX_Cookbook.assets/taxa_func_link_heatmap.png" alt="image-20230728152953911"  />
+    <img src="./MetaX_Cookbook.assets/taxa_func_link_heatmap.png">
 
-<img src="./MetaX_Cookbook.assets/taxa_func_link_bar.png" alt="image-20230728151451213"  />
+<img src="./MetaX_Cookbook.assets/taxa_func_link_bar.png">
 
 - Plot **peptides** in <u>one Function of a Taxon</u>
 
-  <img src="./MetaX_Cookbook.assets/taxa_func_link_pep_heatmap.png" alt="taxa_func_link_pep_heatmap"  />
+  <img src="./MetaX_Cookbook.assets/taxa_func_link_pep_heatmap.png">
 
-  <img src="./MetaX_Cookbook.assets/taxa_func_link_pep_bar.png" alt="taxa_func_link_pep_bar"  />
+  <img src="./MetaX_Cookbook.assets/taxa_func_link_pep_bar.png">
 
 - Switch Bar to Stacked or not ( Line)
 

README.md

@@ -19,45 +19,60 @@ The Tools in OTF Analyzer
 
 ![compostion](https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/composition.png)
 
-## OTFs Network
+## OTFs Examples
 
-Linking Taxa and Functions in different levels of the hierarchy, and different functional categories. e.g., **Species-KO**, **Genus-CAZy**, **Phylum-EC**, etc.
+Linking Taxa and Functions in different levels of the hierarchy, and various functional categories. e.g., **Species-KO**, **Genus-CAZy**, **Phylum-EC**, etc. Lots of visualization tools can be selected.
 
-- ![OTF](https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/tf_link_net.png)
+**Network**
 
+**Dots** represent <u>taxa</u> and **squares** represent <u>functions</u> in the network.
 
+- <img src="https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/tf_link_net.png" alt="OTF" style="zoom: 50%;" />
 
-e.g. The **KEGG Pathways** linked to ***Roseburia hominis***
 
-- ![tf_link_net_2](https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/tf_link_net_2.png)
 
+**Heatmap**
 
+Show all Taxa of a function.
 
-## Download
-### `Desktop Version(Recommended)`:
-The desktop version comes fully set up and ready to use, including all required dependencies and a graphical user interface.
+- <img src="https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/taxa_func_link_heatmap.png" alt="tf_link_heatmap" style="zoom:50%;" />
 
-<a href="https://shiny2.imetalab.ca/shiny/rstudio/metax_download/" target="_blank">Download MetaX Desktop Version</a>
+**Bar**
 
+Show all functions of a taxon
+
+- <img src="https://github.com/byemaxx/MetaX/raw/main/Docs/MetaX_Cookbook.assets/taxa_func_link_bar.png" alt="tf_link_bar" style="zoom:50%;" />
+
+
+
+## Download & Installation
+- **Desktop Version** (Recommended)
+
+  > The desktop version comes fully set up and ready to use, including all required dependencies and a graphical user interface.
+  >
+  > <a href="https://shiny2.imetalab.ca/shiny/rstudio/metax_download/" target="_blank">Download the MetaX Desktop Version</a>
 
 <br>
 
-### `Command-line version`:
-Use [PyPi](https://pypi.org/project/MetaXTools/) to install, then type `metax` in the terminal to launch the GUI.
-  ```bash
-  python -m pip install MetaXTools
-  ```
+- **Command-line version**
 
+    > Use [PyPi](https://pypi.org/project/MetaXTools/) to install, then type `metax` in the terminal to launch the GUI.
+    >
+    > `python -m pip install MetaXTools`
+
+
+
+## Guidebook
 
-## Getting Started
 - `Desktop Version(desktop)`:
   - Refer to the <a href="https://byemaxx.github.io/MetaX/" target="_blank">MetaX Cookbook</a> for detailed instructions on how to use MetaX with the graphical user interface.
   <br>
 - `Command-line version`:
   - Read the example documentation in the [Notebook](https://github.com/byemaxx/MetaX/blob/main/Docs/example.ipynb) for detailed instructions and examples.
 
 
-## Citing MetaX
-- If you use MetaX in your research, please cite the following publication:
-  - **MetaX: A peptide centric metaproteomic data analysis platform using Operational Taxa-Functions (OTF)**. *Wu, Q., Ning, Z., Zhang, A., Zhang, X., Sun, Z., & Figeys, D.* (2024).  bioRxiv. DOI:  <a href="https://doi.org/10.1101/2024.04.19.590315" target="_blank">10.1101/2024.04.19.590315</a>.
+## Citing
+If you use MetaX in your research, please cite the following publication:
+
+> **MetaX: A peptide centric metaproteomic data analysis platform using Operational Taxa-Functions (OTF)**. *Wu, Q., Ning, Z., Zhang, A., Zhang, X., Sun, Z., & Figeys, D.* (2024).  bioRxiv. DOI:  <a href="https://doi.org/10.1101/2024.04.19.590315" target="_blank">10.1101/2024.04.19.590315</a>.