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

The main window has five components:
- The menu bar at the top (See below
for more information about each menu item).
- 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.
- The network management window
(top-left white box).
- The overview window (bottom-left
overview of the network).
- 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
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
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

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:

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.
