Quick Tour of Cytoscape

When a network is loaded, Cytoscape will look something the image below:

Cytoscape Desktop

The main window here has several components:

  1. The menu bar at the top (See below for more information about each menu).
  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 panel (top-left). This contains an optional network overview pane(bottom-left overview of the network).
  4. The main network view window, which displays the network.
  5. The attribute browser panel (bottom panel) which displays attributes of selected nodes and edges and enables you to modify the values of attributes.

The network management and attribute browser panels are dockable tabbed panels known as CytoPanels. You can undock any of these panels by clicking on the Float Window control in the upper-right corner of the CytoPanel.

FloatWindowControl

If you select this control, e.g. on the attribute browser panel, you will now have two Cytoscape windows, the main window, and a new window labeled CytoPanel 2, similar to the one shown below.

CytoPanel2

Note that CytoPanel 2 now has a Dock Window control. If you select this control, the window will dock onto the main window.

Cytoscape also has a set of editors that enable you to build and modify networks interactively by dragging and dropping nodes and edges from a palette onto the main network view window. The editors can be invoked using the Set Editor command on the File menu. An example of a simple biomolecule editor, with the palette contained in CytoPanel 1, is shown below.

Simple BioMolecule Editor

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 PDF). File / Exit closes all windows of Cytoscape and exits the program. File/New opens up a New network for editing. This menu item is disabled until an editor is chosen using the File /SetEditor menu item.

Edit Menu

Edit Menu

The Edit menu Undo and Redo menu items which undo and redo edits made in the Attribute Browser. The menu also 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), as well as an option for deleting selected nodes and edges from the current network. All deleted nodes and edges can be restored to the network via the Edit/Restore Deleted Nodes/Edges menu item. 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 "Command Line Arguments and Properties" for more information.

Data Menu


The Data menu allows you to display or hide the network management panel (CytoPanel 1). It allows you to display or hide the attribute browser (CytoPanel 2), which lets you view and edit attributes assigned to both nodes and edges. (See section 7. Node and Edge Attributes) The Data menu allows you to display an advanced window (contents of CytoPanel 3).

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 2.2

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 of your entire network, which is helpful for navigating very large networks.

Plugins Menu

Plugins Menu

The PlugIns menu has menu items or choices added by plugins that have been loaded, such as "Import BioPAX Document from file".

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

CytoPanels Menu

CytoPanels Menu CytoPanels are floatable / dockable panels which cut down on the number of pop-up windows within Cytoscape. The CytoPanels menu allows you to show or hide CytoPanel 1, CytoPanel 2, or CytoPanel 3 based on the menu item selected.

Note:

In order for these keyboard short-cuts to work, the Cytoscape Desktop Window needs to have the focus. To give the window focus, simply click on it.

Help Menu

Help Menu

The Help menu allows you 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.

Filters

Filters Menu
This menu allows you to bring up a user interface for defining and running filters (see 10. Filters). Filters enable you to extract subnetworks based upon the values of node and edge attributes.

Additional menus may appear, depending on the set of Plugins you have chosen to load.

The Network Management Window

Cytoscape 2.2 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 (top-left tree view in CytoPanel1) 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, seven networks are loaded, six green ones with views and one red one without a view.

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. Networks in the top part of the tree in the figure above were generated in this manner.

The available network views are also arranged as multiple, overlapping windows in the network view window. You can maximize, minimize, and destroy network views by using the conventional window controls for your operating system.

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 or 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