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.

Load and Store Graphs


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:
  1. Load Graph
  2. Save Graph as GML

Zooming


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:

  1. Zoom Out
  2. Zoom In
  3. Zoom Selected Region
  4. 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).

Hide and Show


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

Annotate


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

Set Visual Properties


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

Change Visual Style


Visual styles can be applied to graphs; this operation is specified by the above button.
  1. 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.

Network Layout

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: