Thnaks

Ignore the forst problem - seems to solve itself!

Trying 'V(g)$label <- V(g)$name' I recieve the following error:
        Error in `V<-`(`*tmp*`, value = 0:9) : invalid indexing 

The full code used (with matrix shown) is below - any help appreciated:

> data2
     G1   G2   G3   G4   G5   G6      G7     G8       G9   G10
G1    0    0    0    0    0    0.000   0.000  0.000    0     0
G2    0    0    0    0    0   -0.356   0.000  0.000    0     0
G3    0    0    0    0    0    0.000   0.319  0.000    0     0
G4    0    0    0    0    0    0.000   0.000  0.429    0     0
G5    0    0    0    0    0    0.000   0.000 -0.419    0     0
G6    0    0    0    0    0    0.000   0.000  0.000    0     0
G7    0    0    0    0    0    0.000   0.000  0.000    0     0
G8    0    0    0    0    0    0.000   0.000  0.000    0     0
G9    0    0    0    0    0    0.000   0.000  0.000    0     0
G10   0    0    0    0    0    0.000   0.000  0.000    0     0
> gdata2 <- graph.adjacency(data2, weighted=TRUE, mode="upper")
> E(gdata2)$color <- "green"
> E(gdata2)[ weight<0 ]$color <- "red"
> gdata2$layout <- layout.fruchterman.reingold
> V(gdata2)$label <- V(data2)$name
Error in V(data2) : Not a graph object
> V(gdata2)$label <- V(gdata2)$name
Error in `V<-`(`*tmp*`, value = 0:9) : invalid indexing
> gdata2
Vertices: 10 
Edges: 4 
Directed: FALSE 
Edges:
          
[0] 1 -- 5
[1] 2 -- 6
[2] 3 -- 7
[3] 4 -- 7
> 
-----Original Message-----
From: Gabor Csardi [mailto:[EMAIL PROTECTED]
Sent: 11 July 2008 14:54
To: Dry, Jonathan R
Cc: R Help list
Subject: Re: [R] network


Jonathan, 

please stay on the list. 

The first query i don't understand, can you send a pdf or explain 
a bit what exactly happens.

As for the names, use them as row or column names in the matrix
(see ?colnames), and then do 

V(g)$label <- V(g)$name 

before the plotting.

G.

On Fri, Jul 11, 2008 at 02:47:55PM +0100, Dry, Jonathan R wrote:
> Superb - thanks Gabor
> 
> Two minor queries - firstly the network plot does not seem to fit in the 
> window and so only part of it is plotted.  Secondly, the first row and column 
> of my matrix comprise the sample names - is it possible to show the names in 
> the nodes of the graph (currently it just shows the row number)?
> 
> Your help is much appreciated
> 
> Kind regards
> 
> Jonathan
> 
> -----Original Message-----
> From: Gabor Csardi [mailto:[EMAIL PROTECTED]
> Sent: 11 July 2008 14:33
> To: Dry, Jonathan R
> Cc: r-help@r-project.org
> Subject: Re: [R] network
> 
> 
> I'm sure this is possible with 'network', but i'm not very familiar 
> with that package. In case you don't get an answer on how 
> to do it with network, here is how to do it with the 'igraph' package:
> 
> library(igraph)
> M <- matrix(runif(100)*2-1, 10, 10)
> M[ lower.tri(M, diag=TRUE) ] <- 0
> 
> M[ abs(M) < 0.5] <- 0
> 
> g <- graph.adjacency(M, weighted=TRUE, mode="upper")
> E(g)$color <- "green"
> E(g)[ weight<0 ]$color <- "red"
> 
> g$layout <- layout.fruchterman.reingold
> plot(g)
> 
> Please tell me if something is not clear,
> Gabor
> 
> On Fri, Jul 11, 2008 at 02:04:54PM +0100, Dry, Jonathan R wrote:
> > Hello
> > 
> > I am a relatively new user of R and am struggling to use the 'network' 
> > package.  I have a correlation matrix (produced using 'cor'), and want to 
> > draw a network where each item showing correlation above a threshold (say 
> > 0.5) is joined by a green line, and each item showing correlation below a 
> > threshold (say -0.5) is joined by a red line.  Does anyone have any hints 
> > of how to correctly use functions within the 'network' package to achieve 
> > this?
> > 
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> 
> -- 
> Csardi Gabor <[EMAIL PROTECTED]>    UNIL DGM

-- 
Csardi Gabor <[EMAIL PROTECTED]>    UNIL DGM

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