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

To lay out your network using a Spring Embedded Layout, select Layout Apply Spring Embedded Layout from the main menu. Sample screenshot is provided below:

Figure: Applying the Spring Embedded Layout to a sample network.