Graphics Reference
In-Depth Information
Note
Gephi is available at
https://gephi.org/
.
Links to a quick-start guide
and tutorial as well as plug-ins, and so on, are available from the main
page.
Cytoscape
Cytoscape is another powerful freeware graph analysis and visualization
software package. It was originally developed for analysis of biological data,
but it works for any kind of graph data. Some of the terminology is a bit
different than with other packages. For example, Cytoscape uses
network
to refer to a
graph
and sometimes uses
interaction
to refer to an
edge
.
It has a number of features beyond other packages, such as the capability
to handle multiple links between a pair of nodes, a much wider range of
visual attributes that can be connected to data more flexibly than with other
software, and a variety of plug-ins from the Cytoscape App Store.
Cytoscape Basics
As shown in
Figure 7-19
, Cytoscape presents a straightforward interface
you can use for creating and interacting with the visualization. Toward
the bottom of the screen, a data table, by default, always updates to show
the details for whichever nodes and links are currently selected. In the
visualization window, nodes and links can be selected using the conventions
found in many software packages—that is, click to select, click and drag to
select a block of items, Shift+click to add additional items to the selection,
and Ctrl+click to remove an item from the selection.
