Hmmm, it seems that the colum/row names are not added properly, maybe this works only in the not-yet-released version. You can do
V(gdata2)$label <- colnames(data2) as a workaround. G. On Fri, Jul 11, 2008 at 03:32:15PM +0100, Dry, Jonathan R wrote: > Thnaks > > Ignore the forst problem - seems to solve itself! > > Trying 'V(g)$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 -- Csardi Gabor <[EMAIL PROTECTED]> UNIL DGM ______________________________________________ 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.
