Cytoscape_3/UserManual/Publish

Publish Your Visualizations

When you finish your data analysis and visualization, you need to publish your data to share the results. Cytoscape has several options to do it.

As Session File

The easiest way to share your results with others is simply save everything as a session. You can save your current session into a zipped archive by clicking Save Session icon.

As Images

Cytoscape can generate publication-quality images from network views. By selecting File → Export → Network View as Graphics... you can export the current network view into the following files:

JPG
PNG
PS (Post Script)
SVG
PDF

We recommend to to use PDF for publications because it is a standard vector graphics format and is easy to edit in other applications such as Adobe Illustrator.

Known Issues

For PDF export, there is an option to Export Texts as Fonts. This option does not work for two-byte characters such as Chinese or Japanese. To avoid corrupted texts in the exported images, please uncheck this option when you publish networks including those non-English characters.

As Interactive Web Applications (New in 3.2.0)

These days, web is the platform for data sharing and collaboration. Since version 3.1.0, Cytoscape has Export as Cytoscape.js JSON feature to publish your data for web applications. However, this feature is designed for developers and they have to write some code to set up their web applications to visualize JSON files with Cytoscape.js. It provides maximum flexibility for people who have JavaScript programming experiences, but it is not for end-users. To deliver the versatility of web based visualizations, we have developed a new export option, Export as Interactive Web Visualization, which creates complete web based visualization from your Cytoscape session.

What is an Interactive Web Visualization?

Our definition of interactive web visualization is a browser-based, complete web application to visualize user data just like desktop version of Cytoscape. To accomplish this goal, we use Cytoscape.js and other web technologies to visualize as much information as possible from the original Cytoscape network views. This function simply compresses everything, including your network/table JSON files, visual styles, and template HTML/JavaScript/CSS files into a zipped archive. To publish this as a complete web application, you just need to upload unzipped folder to your web server.

There are two export options: Full and Simple

Full Web Application

Full export option is designed for general users who want to publish their data as a complete single-page application. This application works as a basic viewer for Cytoscape-generated network visualizations on web browsers. Since it is a pure JavaScript application, you can run it on both PCs and tablets.

Simple Network View

This option exports the current network view as a single network view with Cytoscape.js. The purpose of this option is providing a simple boilerplate code for web application developers who want to create custom web applications using Cytoscape.js.

How to Use Exported Archive

Both types of exported archives are simple HTML pages and you can start the application by opening index.html file with your web browser. Due to the browser security setting, you may need to start a local instance of the web server to run the application. Apple Safari allows to run web application from your local file system, but if you use web browsers such as Chrome or Firefox, you need a local web server to check the contents on your machine. The easiest way to setup a local web server is running Python simple HTTP server. If you have Python installed on your machine, just go into the web archive folder and type:

python -m SimpleHTTPServer 8000

and open:

http://localhost:8000/

Of course, once you upload the exported folder to any web servers, everyone can access your visualizations from web browsers.

Here is an example exported file from Cytoscape:

Compatibility

Because we use latest HTML5 based web technologies, we cannot support old web browsers like IE. We strongly recommend to use latest version of modern web browsers such as Google Chrome, Mozilla Firefox, or Apple Safari.

Customize Export Template (For Web Application Developers)

This export option creates minimalistic web application to visualize your network on web browsers. But in some use cases, you may want to use your own page design or add new features to the application. It is possible by editing template code in your configuration directory. The HTML5 template code is stored in ~/CytoscapeConfiguration/web directory. In the web folder, you can find simple and full sub directories. These are the template code for each export option.

Source Code

Simple export template
Full export template