Hello all, I am brand new to this list; forgive me if I mis-step! I am relatively new, also, to R, which I am using in conjunction with an open source java network visualization tool, cytoscape (see http://www.cytoscape.org). We have lots of whole-genome,high throughput biological data -- microarray, ICAT, MPSS -- and R (of course!) is very useful in exploring these data. I wonder: has this group defined an R data structure for representing network graphs, with nodes and edges (and perhaps with node and edge attributes as well)? I wish to include this view of our data along side our experimental data. Thank you, - Paul Shannon Institute for Systems Biology Seattle
[R--gR] R data structure for network graphs?
3 messages · Paul Shannon, Giovanni Marchetti, Jeremy Semeiks
On Thursday 18 December 2003 15:24, Paul Shannon wrote:
I wonder: has this group defined an R data structure for representing network graphs, with nodes and edges (and perhaps with node and edge attributes as well)? I wish to include this view of our data along side our experimental data.
Dear Paul I think that the only structure available in R for graphs is class graph defined in package graph by Robert Gentleman. It is a Bioconductor package. Look at http://www.bioconductor.org/ Package: graph Description: A package that implements some simple graph handling capabilities. Version: 1.1.9 Author: R. Gentleman, Elizabeth Whalen Maintainer: R. Gentleman Dependencies: R (>= 1.7), cluster, XML SystemRequirements: NA License: LGPL Giovanni
< Giovanni M. Marchetti > Dipartimento di Statistica, Univ. di Firenze Phone: +39 055 4237 204 viale Morgagni, 59 Fax: +39 055 4223 560 I 50134 Firenze, Italy email: gmm at ds.unifi.it
On Fri, Dec 19, 2003 at 12:00:26PM +0100, Giovanni Marchetti wrote:
On Thursday 18 December 2003 15:24, Paul Shannon wrote:
I wonder: has this group defined an R data structure for representing network graphs, with nodes and edges (and perhaps with node and edge attributes as well)? I wish to include this view of our data along side our experimental data.
Dear Paul I think that the only structure available in R for graphs is class graph defined in package graph by Robert Gentleman. It is a Bioconductor package. Look at http://www.bioconductor.org/
Bioconductor also provides the RBGL class, which is based on the C++ Boost graph libraries. RBGL provides some basic graph algorithms as well. But I find it to be fairly slow for large graphs. - Jeremy