How to produce high quality Network Figures

You can produce high quality Network Figures either using cytoscape or meduza programs.


You can use online cytoscape capabilities to align and edit your network. Please use Controls menu in the right top corner (cytoscape online). You can select several layout options (use menu Layout). We recommend to try several layout options ("cola", "cose", etc). You can save your model either as image (.png) or JSON format. The JSON file can be opened and edited by cytoscape on your computer.

Example of the figure prepared with online cytoscape is presented in figure 1.

Figure 1. Example of network model


If you do not have Cytoscape you can use Medusa - a Java application for visualizing and manipulating graphs of interaction to visualize your network model.
Click here to download Medusa.jar program for network visualization.

Color and Shape Legends.

Colors are used to indicate pathway attribute for some genes. You can find color-pathway relationships directly in the model. Node Shapes:
rectangle - the gene from the input list 1.
circle - the gene from the input list 2.
diamond - the gene was in input list 1 and 2.
triangle - missing genes (added to connect input genes)

Step 1. Download Nework Model

Click on "Medusa Model" field,
Select All text (CTRL+A) from the field "Medusa Model".
Copy (CTRL+C) and save it into the file ("mymodel.txt") at your computer (as .txt).

Step 2. Open File

Run Medusa.jar application.
Go to menu "File-new".
Select the file "mymodel.txt" previously saved and open it.
Click on "Relax" button.

Step 3. Layout of the network

You need to perform the layout of the network manually.
First, we recommend to press "Relax button" and to shake your model (select a node with a mouse and shake it).
Second, we recommend to select an appropriate scale (in the right -low corner there is a possibility to scale your model by moving the scale pointer from 0 to 300, the default value 100 ).
After these steps press again relax button and perform layout manually.

After finishing layout save your model (Go to menu "File-save").
If you open this file next time with medusa it will have the same layout.

Step 4. Exporting your model into high-quality images

You can convert the model into high-quality images by exporting (go to menu "File-export") the file to Image (.jpg , .png) or PostScript (.ps or .eps) formats.