Navigation and Layout
Toolbar

General graph loading, saving, editing, viewing and annotation operations are
available from the toolbar.
These functions and the buttons which select each function are described below.

Graphs can be loaded from the file system in SIF and GML formats, or saved in
GML format. The toolbar buttons for loading and save graphs, from left to right:
- Load Graph
- Save Graph as GML

Graphs or regions of graphs can be viewed at higher or lower magnification, and appear closer or further. The four zoom buttons are used to select the zooming
behavior.
Use the zooming buttons located on the toolbar to zoom in / out of the
interaction network shown in the current network
display. Zoom icons are detailed below, from left to right:
- Zoom Out
- Zoom In
- Zoom Selected Region
- Zoom Out to Display all of Current Network
You can also zoom in/out by holding
down the right mouse button and moving the mouse to the right (zoom
in) or left (zoom out).

Nodes and edges in the graph can be hidden or shown; these operations are
selected from the hide/show buttons. From left to right:
- Show All Nodes and Edges
- Hide Selected Region

Nodes can be annotated with loaded annotations; this operation is specified by the above button:
- Add Annotation Ontology to Nodes

New visual styles can be created and edited; this operation is specified by
the above button.
- Set Visual Properties

Visual styles can be applied to graphs; this operation is specified by the
above button.
- Change the Current Visual Style
Node Selection
Use the left mouse button to select
a node (hold down the Shift key to select more than one node). Use
the right mouse button to launch a context sensitive menu with
additional information about the node that was clicked on.
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.
Some of the layout algorithms provided with Cytoscape 2.2 are:
Cytoscape Spring-embedded Layout
Spring-embedded layout is based on a "force-directed" paradigm. Network
nodes are treated like physical objects that repel each other, such as electrons.
The connections between nodes are treated like metal springs attached to the pair
of nodes. These springs repel or attract their end points according to a force
function. The layout algorithm sets the positions of the nodes in a way
that minimizes the sum of forces in the network.
To lay out your network in Cytoscape using a Spring Embedded Layout,
select Layout => Apply Spring Embedded Layout from the main menu.
A sample screen shot is provided below:

yFles Circular Layout
This algorithm produces layouts that emphasize group and tree structures within a
network. It partitions the network by analyzing its connectivity structure, and arranges the partitions as separate circles. The circles themselves
are arranged in a radial tree layout fashion:

yFiles Hierarchical Layout
The hierarchical layout algorithm is good for representing main direction
or flow within a network. Nodes are placed in hierarchically arranged
layers and the ordering of the nodes within each layer is chosen in such
a way that minimizes the number of edge crossings:

yFiles Organic Layout
The organic layout algorithm is a kind of spring-embedded algorithm
that combines elements of the other algorithms to show the clustered
structure of a graph:

Scaling and Rotation
Cytoscape provides operations for scaling and/or rotating networks or
segments of networks. The figure below shows the network view from
the organic layout, with the selected nodes scaled by a factor of 1.5
and rotated by 90 degrees:
