Quick Tour of Cytoscape

When a network is loaded, Cytoscape will look something like this:

Cytoscape Desktop

The main window has five components:

  1. The menu bar at the top (See below for more information about each menu item).
  2. The toolbar, which contains icons for commonly used functions. These functions are also available via the menus. Hover the mouse pointer over an icon and wait momentarily for a description to appear as a tooltip.
  3. The network management window (top-left white box).
  4. The overview window (bottom-left overview of the network).
  5. The main network view window, which displays the network.

The Menus

File Menu


The File menu contains most basic file functionality: File / Load for loading a variety of file types; File / Save for saving. File/Help displays a credits screen. File / Print allows printing. File / Export As... allows you to export to a file in a number of graphics formats (such as postscript). File / Exit closes all windows of Cytoscape and exits the program.

Edit Menu

Edit Menu

The Edit menu contains a Squiggle feature that enables you to mark up your network. This can be particularly useful during live presentations. There are also options for creating and destroying views (graphical representations of a network) and networks (the network data – not yet visualized). The Edit Menu also supports Preferences editing for properties and plug-ins via a Preferences Dialog. Preferences editing operates on the cytoscape.props file associated with the user’s instance of Cytoscape. See “Commands Line Arguments and Properties” for more information.

Data Menu


The Data menu allows you to display the attribute browser, which lets you view attributes assigned to both nodes and edges. See "Node and Edge Attributes" fo rmore information.  Other options shown relate to plugins which are packaged with Cytoscape 2.1.

Select Menu


The Select menu contains methods and operations for selecting nodes and edges, and using the current selection to create a new network and an associated view.

Layout Menu


The Layout menu has an array of features for organizing the network visually according to one of several algorithms, aligning and rotating groups of nodes, and adjusting the size of the network. Most of these features are available from plugins that are packaged with Cytoscape 2.1

Visualization Menu


The Visualization menu provides options for changing the mapping from biological data to a visual representation: colors of nodes, thickness of edges, etc. These features are explored in-depth in the 9. Visual Styles section. This menu also provides an Overview (Bird’s Eye view) of your entire network, which is helpful for navigating very large networks.

PlugIns Menu

Plugins Menu

The PlugIns menu has menu entries or choices added by plugins that have been loaded, such as "Find Enriched Attributes".

Note: A list of Cytoscape PlugIns with descriptions is available online at: http://cytoscape.org/plugins2.php

Filters Menu

This menu has been added by the plugin in the file "filter.jar". The function of this plugin is not described further in this manual. Additional menus may appear, depending on the set of PlugIns you have chosen to load.

Help Menu

Help Menu

The Help menu allows users to launch the online help viewer and browse the table of contents (Contents…), or view the help text associated with a context-sensitive selection (Context Sensitive…). By selecting Context Sensitive… menu item and then selecting a GUI component, the help related to the selected item is launched. The “About…” menu item displays information about the running version of Cytoscape.


The Network Management Window

Cytoscape 2.1 allows multiple networks to be loaded at a time, either with or without a view. A network stores all the nodes and edges that are loaded by the user and a view displays them. You can have many views of the same network. Networks (and their optionally associated views) can be organized hierarchically.

An example where a number of networks have been loaded and arranged hierarchically is shown below:

Network Management Window


The network manager (upper left panel) shows the networks that are loaded. Clicking on a network here will make that view active in the main window, if the view exists (green highlighted networks only). Each network has a name and size (number of nodes and edges), which are shown in the network manager. If a network is loaded from a file, the network name is the name of the file.

Since some networks are very large (thousands of nodes and edges) and can take a long time to display. For this reason, a network in Cytoscape may not contain a ‘view’. Networks that have a view are highlighted in green and networks that don’t have a view are highlighted in red. You can create or destroy a view for a network by right-clicking the network name in the network manager or by choosing the appropriate option in the edit menu. You can also destroy previously loaded networks this way. In the picture above, five networks are loaded, three green ones with views and two red ones without views.

Certain operations in Cytoscape will create new networks. If a new network is created from an old network, for example by selecting a set of nodes in one network and copying these nodes to a new network (via the Select->To New Network option), it will be shown as a child of the network that it was derived from. In this way, the relationships between networks that are loaded in Cytoscape can be seen at a glance.

The available network views are also shown as tabs on the top of the view window. You can click on the tab to go to the named network and the network manager will update accordingly. Advanced users: Cytoscape also has two viewing modes that alter the way in which these windows are displayed. This mode can only be selected on startup of the program by adding the –t option on the command line (see section 4. Command Line Arguments).

The Network Overview Window

The network overview window shows an overview (or ‘bird’s eye view’) of the network. It can be used to navigate around a large network view. This feature can be turned on an off via the Visualization menu. The red-outlined blue rectangle in the overview window shown below can be dragged with the mouse to navigate to a part of the network. The size of the navigation rectangle depends on the size of the active view and the zoom level of the view. The rectangle is smaller if the view is zoomed in and larger if zoomed out.

Network Overview