21. Export Your Data¶
21.1. Raw Data Export¶
To use data from Cytoscape networks in an external application, the data has to be exported. As a Cytoscape network consists of a number of different types of data, there are options in Cytoscape for each exportable data type. These options (Network, Table, Styles) can be found on the File → Export submenu (shown above).
Network Data Exchange (NDEx) Public Database¶
The Network to NDEx and Collection to NDEx options are used to store a network on a public NDEx server. You can use an NDEx server as a cloud-based store for your networks, as a means of sharing networks with collaborators, or to archive networks for publication. To store a network, you must have an NDEx account, which you can create by visiting the NDEx Public Server website.
The Network to NDEx option saves only the currently selected network to your NDEx account. Such networks are suitable for processing by other applications and web services, as they contain only the nodes and edges in the selected network – other networks and the nodes and edges unique to them are not written. If you import this network (using the Cytoscape Search bar), only the single network will be loaded.
The Collection to NDEx option saves all networks in the collection containing the currently selected network. If you import this collection (using the Cytoscape Search bar), the entire collection will be loaded. This option is closest to saving an entire Cytoscape session, except that only the current collection is saved.
When you select either option, the CyNDEx-2 Browser dialog will appear and enable you to provide metadata that will be displayed during subsequent NDEx searches. To save a network, you must add an NDEx account profile to the CyNDEx-2 Browser (by filling out the profile form reachable by clicking on the Anonymous credential in the upper right), and then make it current.
You can set the name of your network by editing the Network Name attribute at the bottom. The Save as a New Network option enables you to create a new network instead of overwriting an existing NDEx network of the same name. If you choose to make your network public, you must fill in the Version and Description attributes. Choose the Save as Public option to enable collaborators to load your network.
When the export to NDEx is complete, you will be given an opportunity to capture the network’s UUID in your clipboard. The UUID is suitable for e-mailing to colleagues so they can load your network via their Cytoscape Search bar (provided you selected the Save as Public option). For more sharing options, see the NDEx Public Server website.
Further information on NDEx is available at the NDEx Informational/Doc website.
The Network option is used to export network data. Network data includes the nodes and edges in the network, and also will include data attributes and visual information if the chosen format supports it (like XGMML). Network data can be exported in a number of formats, including:
- SIF (Simple Interaction Format)
- NNF (Nested Network Format)
- PSI-MI Level 1 and 2.5
- Cytoscape.js JSON (can be used with Cytoscape.js, a tool described in future sections)
- CX JSON (for Cytoscape Cyberinfrastructure network exchange)
The default format is SIF, which is a simple tab-delimited network format that provides node names and edge interactions only. You can choose the format using the dialog drop-down box. A file name is automatically suggested based on the network name and selected format, with the file path defaulting to the current working directory. You can change the suggested file name/path using the text box or Browse button. Press OK to export with the selected options.
The Table option is used to export any of the data tables that are available in the current Cytoscape session. This includes the node, edge, and network tables that can be seen in the Table Browser, as well as any unassigned tables. The only currently supported file format currently for export is CSV (comma-separated value).
The export dialog for Table has only two selectable options - the table to export and the file name (file type is always CSV). A file name is suggested based on the name of the selected table with the path defaulting to the current working directory. As in Network, the suggested file name can be changed using the Browse button or the text field. Press OK to export the selected table with the given file name.
The Styles option is used to export one or more visual styles available in the current Cytoscape session. Supported formats include Style XML (which can be imported by 3.x versions of Cytoscape) or Cytoscape.js JSON (which can be used with Cytoscape.js, described in future sections).
Style export has three options - the export format (as described above), the style(s) to export, and the file name (a suggestion will be made based on the current directory and file type). As in Network → Table, the suggested file name can be changed using the Browse button or the text field. The list of styles is a multiple-selection list - one or more can be selected using Ctrl/Cmd-click (to select multiple discontiguous elements) or Shift-click (to select a contiguous element range). Press OK to export all selected styles with the given file path.
21.2. Exporting for Publication¶
When you finish your data analysis and visualization, you can publish your data to share the results. Cytoscape has several options to do this, with most options suitable for Cytoscape users and other options suitable for programmers wanting to create unusual or complex network viewers. These are further explained below.
- An NDEx network
- A session file
- A static image
- An interactive web application
- Full web application
- Simple network view (for web application developers)
As an NDEx Network¶
The easiest way to share your results with others is to save your network in the NDEx Public Database by using the Network to NDEx or Collection to NDEx options. When you save your network, you will receive a UUID (e.g., 50e3dff7-133e-11e6-a039-06603eb7f303) that you can e-mail to collaborators for use in their own Cytoscape Search bar (provided you exported using the Save as Public option – see the Save as Public option.)
NDEx also has options that enable you to:
- generate a DOI suitable for use in publications
- create an anonymous sharable link (similar to a Google Doc shared link)
- create interest groups and specific sharing within NDEx
As a Session File¶
Another easy way to share your results with others is simply saving everything as a session file (which is a zipped session archive). You can save your current session by clicking the Save Session icon. You can save to a thumb drive, a shared file system, or even a cloud drive directory such as Dropbox. If you save to a shared drive, beware not to have two people work on the same session file with Cytoscape at the same time, as unpredictable results may occur.
As a Static Image¶
Cytoscape can generate publication-quality images from network views. By selecting File → Export as Image..., you can export the current network view into the following formats:
- PS (Post Script)
The image export dialog has a variable number of options based on the file format selected, with file type and file name always being selectable. PNG and JPEG have options for scaling, while other formats only have a single option, Export Text as Font. The file name is suggested based on the name of the selected table with the path defaulting to the current working directory. As in raw data export, the suggested file name can be changed using the Browse button or the text field. Press OK to export an image with the given file name and parameters.
We recommend using PDF for publications because it is a standard vector graphics format, and it is easy to edit in other applications such as Adobe Illustrator.
For PDF export, there is an option to Export text as font. 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 an Interactive Web Application (New in 3.2.0)¶
The Web is an excellent platform for data sharing and collaboration, and Cytoscape provides a number of ways to publish your network on the web, with each choice representing tradeoffs between ease, simplicity, and customization options. All solutions leverage the cytoscape.js drawing library, and so enable not only viewing but also Cytoscape-style interactive browsing of networks and attributes.
The simplest choice is CyNetShare, where you save your network (and optionally a style) on a public file system, then interactively view the network in a browser. Like Google Maps, you can generate and publish a URL that allows collaborators to also view your network.
Alternatively, Cytoscape can generate an entire web site showing a single page containing the viewer with your network pre-loaded. You can load this directly onto your own web server to become part of your web site.
These features are available as Export menu items under the File menu, and are described in sections below.
For example, here is a network in Cytoscape:
Here is the same network as an interactive web visualization:
Note that web browsers can render small networks (e.g., 1000 nodes) quickly and effectively, but attempting to render large ones (e.g., 5000 nodes) will take a very long time.
A word about exporting styles to interactive web applications: Our web applications are based on the cytoscape.js display library, which renders a subset of Cytoscape styles. For more information, see the Export Styles to Cytoscape.js section below.
Generating a Full Web Application¶
To generate an entire web page for all networks in the session as a zip archive, select File → Export as Web Page.... The following dialog will appear:
This simple dialog has only two options - the file name and the type of web export (full, simple network view, or JSON). For full web application, we use the default. The file name is suggested based on the name of the selected table with the path defaulting to the current working directory. As in raw data export, the suggested file name can be changed using the Browse button or the text field. Press OK to export a web archive with the given file name.
To view the web page, unzip the archive into a folder on your PC or web server. The folder will contain an index.html file, the network data, and other files. You can open the index.html file in your browser (usually from your browser’s File → Open menu item.)
Note: Depending on your browser’s security settings, you may not be able to open the index.html file directly if it is stored on your PC. Attempting to do so may result in an empty browser window. To display the web page on your PC, you can install the CyWebrowser app, then view the index.html file inside of its browser window.
Alternately, you can start a local web server on your PC. An easy way to do this is by running the 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 use your browser to open:
Testing the archive on your PC will serve as an easy test of the web page, but to publish it to collaborators, you should unzip your archive onto a web server.
Here is an example exported file from Cytoscape:
Note that because Cytoscape uses the latest HTML5-based web technologies, it cannot support older or non-conformant web browsers such as Internet Explorer. We strongly recommend using the latest version of modern web browsers such as Google Chrome, Mozilla Firefox, or Apple Safari.
Generating a Simple Network View (For Web Application Developers)¶
To generate a web page for a single network view as a zip archive, select File → Export as Web Page ... as before, but this time choose the Simple viewer for current network only format as below:
Everything else works as before, though this time the viewer will only include the current network. Press OK to proceed with the export.
For instructions on testing the customized web application, see Generating a Full Web Application above.
Customize Export Template (For Web Application Developers)¶
The code generated by Cytoscape for the Full Web Application and the Simple Network View web applications is minimalistic. While you can directly modify this code yourself to create your own page design or add new features, the modifications will apply to a single exported network. If you are a web application developer, you can change the application code generated for all exports by editing HTML5 template code resource files in your ~/CytoscapeConfiguration/web directory:
In this folder, you can find full and simple sub directories corresponding to Full Web Application and the Simple Network View described above.
To build these project, you need the following tools installed:
Full Export Template¶
This is an AngularJS based web application built with grunt (at least for now – we have plans to migrate to gulp). Source code and more documentations are available here:
To build the project into dist directory, type:
Simple Export Template¶
This template is generated by a simple gulp project. The source code is available here:
To build the project into dist directory, type:
Use Your Custom Templates for Export¶
Once you have your own builds, you can deploy your templates by replacing the contents of full and simple with your own builds.