How to produce high-quality images

In the case of spider tools (KEGG spider, PPI spider, R spider, Ccancer spider) the network models are provided. The online visualization capabilities are limited. In addition, to create high-quality images of the network models you need to download them and use locally Cytoscape or Meduza program (Cytoscape and Meduza are free programs. Before using them you need download and install Cytoscape or Meduza program (follow links on result page)).

You need to perform 4 simple steps to create high quality figures using these programs. Please, read instructions below.





Cytoscape

Step 1. Download file

Click on the corresponding link to download files in ".xgmml". Simply save the file on your computer. Please, specify the same file extension (".xgmml").

Step 2. Open File

Start Cytoscape program on your computer. Go to menu "File->Import->Network(Multiple file types)". Select the file (".xgmml") downloaded previously and open it. Please note that the file should have extension ".xgmml".

Step 3. Layout of the network

Go to menu "Layout->yfiles->organic". You can also try the other multiple layout options.

Step 4. Exporting your model into high-quality images

Go to menu "File->Export->Network view as Graphics" and select appropriate format.





Medusa

Step 1. Download file

Click on the corresponding link to download Meduza file. Simply save the file on your computer.

Step 2. Open File

Go to menu "File-new". Select the file downloaded previously and open it.

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.