[R] Graph visualization

[Steve Lianoglou]

Hi,

On Sep 11, 2009, at 8:22 AM, Arber Ngjela wrote:

> Hello,
> I am working with graph and adjacency matrix, the package 'graph'  
> seems to be appropriate for this.
> An example in the package
>> mat <- rbind(c(0, 0, 1, 1),
> +              c(0, 0, 1, 1),
> +              c(1, 1, 0, 1),
> +              c(1, 1, 1, 0))
>> rownames(mat) <- colnames(mat) <- letters[1:4]
>> graph1 <- new("graphAM", adjMat=mat)
>> graph1
> A graphAM graph with undirected edges
> Number of Nodes = 4
> Number of Edges = 5
>
>
> how can I plot the object graph1?

I haven't used the graph library, but I do use the igraph library a  
bit and it's quite good (highly recommended). There is a tkplot  
function implemented which not only plots your graph, but allows you  
to pull/push nodes around on the screen, select, etc (you'll need the  
tcl/tk stuff installed).

Like so:
library(igraph)
mat <- rbind(c(0, 0, 1, 1),
               c(0, 0, 1, 1),
               c(1, 1, 0, 1),
               c(1, 1, 1, 0))
dimnames(mat) <- list(LETTERS[1:4], LETTERS[1:4])
graph <- graph.adjacency(mat)
tkplot(graph)

(you can specify different layouts, too).

HTH,
-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact