4. Quick Tour of Cytoscape

This chapter describes the basic layout and mechanics of using Cytoscape. If you would prefer to learn by doing, consider starting with the Basic Expression Analysis Tutorial.

4.1. Starter Panel

When you start Cytoscape, you can access basic functions from the Starter Panel:

The Starter Panel is designed to give you quick access to a set of sample session files, as well as tutorials and Cytoscape news. The sample session files include a broad range of networks to give a sense of the diversity of interaction types, visualization styles and biological applications (see Network Table properties for more information about each sample session network). The Starter Panel will also present your own most recent sessions for quick access.

When you load a session file, the Starter Panel will disappear. You can display it at any time by choosing View → Show Starter Panel.

For information on user privacy, see the Cytoscape Privacy Policy.

4.2. Basic Features

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

Most functionalities are self-explanatory, but we’ll go through a concise explanation for clarity. The main window here has several components:

  • The Menu Bar at the top (see below for more information about each menu).

  • The Tool Bar, 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. Right-clicking on the tool bar allows the contents to be customized.

  • The Network Panel (Network panel of the Control Panel). At the top of the Network Panel is a Search bar, with direct access to multiple external resources.

  • The main Network View Window, which displays the network. At the bottom of the network view are a set of network view tools.

  • The Table Panel (bottom right panel), which displays columns of associated data for nodes, edges and network-wide, and enables you to modify the values of column data.

The Network Panel and Table Panel are dockable tabbed Panels. You can undock any of these panels by clicking on the Float Window control in the upper-right corner of each panel. This is useful when you want assign the network panel as much screen space as possible. You will now have two Cytoscape windows, the main window, and a new window labeled Table Panel, similar to the one shown below. A popup will be displayed when you put the mouse pointer on a cell.

To dock the window again, click the Dock Window icon .

Clicking the Minimize icon will minimize the panel; the panel can be shown again by choosing View → Show and selecting the relevant panel, or by clicking on one of the tabs in the minimized panel, for example Network or Node Table, and then clicking the Dock icon.

For more information on the panels in Cytoscape, see the Panels section.

Network Editing

Cytoscape also has an edit functionality that enables you to build and modify networks interactively within the network canvas. To edit a network, just right-click on the open space of network window, select the menu item Add → Node, a new node will be added to the canvas. To add an edge, right click on a node, choose the menu item Edit → Add Edge. Then select the target node, a new edge will be added between the two nodes. In a similar way annotation objects can be added; pictures, shapes or textboxes; much like in MS PowerPoint or similar software. Detailed information on network editing can be found in the Editing Networks section.

4.3. The Menus

File

The File menu contains most basic file functionality: File → Open Session for opening a Cytoscape session file; File → New Network for creating a new network, either blank for editing, or from an existing network; File → Save for saving a session file; File → Import for importing data such as networks and tables; and File → Export for exporting data. File → Export Network to Image lets you export the network in either JPEG, PDF, PNG, PostScript or SVG format. File → Export Network to Web Page lets you export the entire session or a single network as a Web page using Cytoscape.js.

File → Open Recent Session will list recently opened session files for quick access. File → Print… allows printing.

Edit

The Edit menu contains Cut, Copy and Paste functions, as well as Undo and Redo functions which undo and redo edits made in the Table Panel, edits to the network and to layout. The Undo/Redo functions work on the last 10 tasks performed.

There are also options for creating and destroying views (graphical representations of a network) and networks (the raw 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 Edit → Undo.

Other editing options include; Remove Duplicated Edges will delete edges that are duplicates (having the same source and target nodes), keeping one edge, Remove Self-Loops removes edges that have the same source and target node, and Delete Selected Nodes and Edges… deletes a selected subset of the network. Rename Network… allows you to rename the currently selected network.

A set of functions for bringing annotations forward, backward etc, and pushing/pulling them to the foreground vs background layer are also available in the Edit menu.

Editing preferences for properties and apps are found under Edit → Preferences → Properties…. More details on how to edit preferences can be found here.

View

The View menu allows you to display or hide panels, including the Control Panel, Table Panel, Result Panel, Tool Panel and the Command Panel. In addition, it also provides a means for viewing the Starter Panel. It also provides the control of other view-related functionality.

Select

The Select menu contains different options for selecting nodes and edges.

Layout

The Layout menu has an array of features for visually organizing the network. The features in the top portion of the network (Bundle Edges, Clear All Edge Bends, Node Layout Tools) are tools for manipulating the network visualization. The bottom section of the menu lists a variety of layout algorithms which automatically layout a network.

Apps

The Apps menu gives you access to the App Store (Apps → App Store) for managing (install/update/delete) your apps and may have options added by apps that have been installed. Depending on which apps are loaded, the apps that you see may be different than what appear here. The below picture shows a Cytoscape installation without installed apps.

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

In previous versions of Cytoscape, apps were called plugins and served a similar function.

Tools

The Tools menu contains advanced features like Enrichment Table, cyChart, Analyze Network, Open web page, Merge, Execute Command File…, Job Status Monitor and Diffuse.

Cytoscape Web Browser allows for viewing any html page directly in Cytoscape. The web browser can be opened in a separate window or can be launched in the Results Panel.

Help

The Help menu allows you to launch the online help viewer and browse and search this manual. It also provides direct access to a Tour of Cytoscape, as well as a full listing of Cytoscape tutorials. Tutorial content opens automatically in the Cytoscape Web Browser. Video demos are also linked to direclty from the Help menu.

The Citations option displays the main literature citation for Cytoscape, as well as a list of literature citations for installed apps. The list will be different depending on the set of apps you have installed.

The Help menu also allows you to connect directly to Cytoscape Help Desk and the Bug Report interface.

4.4. Network Management

Cytoscape 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.

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

The network manager (in the Control 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.

  • Each network has a name and size (number of nodes and edges), which are shown in the network manager. The number of nodes and edges is shown by default but this can be disabled under Options → Show Number of Nodes and Edges.

  • If a network is loaded from a file, the network name is the name of the file. The list of networks can be sorted alphabetically by network name by clicking on the Options button at the top right and selecting Sort Network by Name.

  • By default, the network provenance history is also shown in the Network Panel, for example showing if a network originated as a subnetwork from another network. This can be disabled under Options → Show Network Provenance History.

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 in normal black font 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.

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 File → New Network option), it will be shown immediately follows the network that it was derived from.

Network views can also be detached (undocked) from the main Cytoscape window. When detached, a view window can be dragged to another monitor, resized, maximized and minimized by using the normal window controls for your operating system. Notice, however, that closing a view window does not destroy it, but simply reattaches it to the Cytoscape window.

Arrange Network Windows

When you have detached network view windows, you can arrange them by selecting one of these options under View → Arrange Detatched Views:

Grid

Cascade

Vertical Stack

Side by Side

4.5. Network View Tools

At the bottom of the Network View Window is a set of network tools:

  • Show Grid will arrange all loaded networks as a grid.

  • Show Network will show the currently selected network.

  • Detach View detaches the network view window from the main Cytoscape window.

  • Export to File… gives you options to export the network or image.

  • Always Show Graphics Details forces the rendering of graphics details. It is turned off by default.

  • Toggle Node Selection allows you to turn off/on node selection. It is turned on by default.

  • Toggle Edge Selection allows you to turn off/on edge selection. It is turned on by default.

  • Toggle Annotation Selection allows you to turn off/on annotation selection. It is turned off by default.

  • Toggle Label Selection allows you to turn off/on node/edge label selection. It is turned off by default.

  • Hide Navigator lets you hide the Navigator (“bird’s eye view”).

The Navigator (or bird’s eye view) shows an overview of the network. It can be used to navigate around a large network view. The blue rectangle indicates the portion of the network currently displayed in the network view window, and it can be dragged with the mouse to view other portions of the network. Zooming in will cause the rectangle to appear smaller and vice versa.