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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