Hello gRers,
In the (well-attended) session on gR at the JSM meeting in Toronto in
August I mentioned that other researchers have developed quite powerful
open source tools for displaying, and interacting with, graphs. Below I
include some more information on two such packages.
(1) Cytoscape
http://www.cytoscape.org
<info from the web-page and elsewhere>
Cytoscape is a cross-platform open source bioinformatics software platform for
visualizing molecular interaction networks and integrating these
interactions with gene expression profiles and other state data.
* Customize network data display using powerful visual styles.
* Visualize a superposition of continuous and discrete variables on the
network nodes and edges. For example, expression data can be
mapped to node color, label, border thickness, or border color,
etc. according to user-configurable colors and visualization
schemes.
* Browse various attributes of network nodes and edges.
* Layout networks in two dimensions. A variety of layout algorithms
are available, including cyclic and spring-embedded layouts.
Layouts may be tweaked by hand.
* Zoom in/out and pan for browsing the network.
* Use the network manager to easily organize multiple networks.
* Use the birds eye view to easily navigate large networks.
* Use a wide range of pre-written "plug-ins"
http://cytoscape.org/plugins2.php
to perform analyses and manipulations of the networks.
For example, there is a plug-in (cytotalk) that allows an R session
to directly interact with and manipulate a Cytoscape network, using
the Bioconductor RSJava package.
See: http://www.bioconductor.org
(Thanks to David Reiss, from the Institute for Systems Biology.)
(2) Zoomgraph is another visualization package developed by HP labs:
http://www.hpl.hp.com/research/idl/papers/zoomgraph1/
Best wishes,
Thomas Richardson