Thank you so much Gabor for your reply. I had spotted your post earlier and it
worked like a charm. Interestingly I have just ran into a trouble with the
stament dend <- igraph:::as.dendrogram.igraph.walktrap(fc). Apparently the
members are empty as when I print(dend) it says 'dendrogram' with 2 branches
and members total, at height 93" while the error with using dend with
dendrapply remians to be
Error in `[[.dendrogram`(X, 2L) : attempt to set an attribute on NULL
Any ideas?
My code looks like this
File2Open = paste(FilePath, "NetworkFiles\\net\\", NetPrefix, "
", TPPostfix, ".net", sep = "")
g <- read.graph(File2Open, format="pajek")
g <- delete.isolates(g)
g <- simplify(g)
fgc <- fastgreedy.community(g, modularity=TRUE, weights =
E(g)$weight)
ModularityIndexfgc <- max(fgc$modularity) # fgc modularity
ModularityIndexng <- modularity(g, membership, weights =
E(g)$weight) # newman-girvan modularity
dend <- igraph:::as.dendrogram.igraph.walktrap(fgc)
png(filename = paste(FilePath,
"Analysis\\Graphs\\EColiStressModuleHeatMap", NetPrefixAbbr, TPPostfix, ".png",
sep = ""), width = 800, height = 800) # heat map is square
adjMatrix = get.adjacency(g, attr="weight")
DendNodeCounter <- 0 # counter for ColorGroupsOrdered
ColorGroupsOrdered <- rep("red", vcount(g))
dendrapply(dend, colLab) # modifies ColorGroupsOrdered
________________________________________
From: csardi.ga...@gmail.com [csardi.ga...@gmail.com] on behalf of Gábor Csárdi
[csa...@rmki.kfki.hu]
Sent: Thursday, May 31, 2012 10:45 AM
To: Aziz, Muhammad Fayez
Cc: r-help@r-project.org
Subject: Re: [R] community finding in a graph and heatplot
On Tue, May 29, 2012 at 1:16 AM, Aziz, Muhammad Fayez
<az...@illinois.edu> wrote:
>
> Hi everyone,
>
> I am using the fastgreedy.community function to get the $merges matrix and
> the $modularity vector. This serves my purpose of testing modularity of my
> graph. But I am "greedy" to plot the heat map and dendrrogram based on the
> $merges dendogram matrix. I know that heatplot does the graphics part but I
> am not sure if the dendogram generated by the heatplot will match the one
> given by fastgreedy.community in all cases and that the heat map will
> represent the same clustering.
No, they are different. To plot fast-greedy results as a dendrogram,
see this and the follow-ups:
http://lists.gnu.org/archive/html/igraph-help/2010-11/msg00059.html
Gabor
> Tell me if my apprehension is incorrect. Otherwise please let me know of any
> alternatives. Here is the code I am testing so far:
>
> # http://igraph.sourceforge.net/doc/R/modularity.html
> # http://igraph.sourceforge.net/doc/R/fastgreedy.community.html
> # http://igraph.sourceforge.net/doc/R/graph.constructors.html
>
> library(igraph)
> library(made4)
>
> g <- graph(c(1,2, 2,3, 3,1, 4,5)-1, , FALSE)
> print(g)
> ModuleInfo <- fastgreedy.community(g)
> print(ModuleInfo)
> heatplot(c(1,2, 2,3, 3,1, 4,5))
>
>
> Thanks
> Fayez
> Grad student UIUC
> IL, USA
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
--
Gabor Csardi <csa...@rmki.kfki.hu> MTA KFKI RMKI
______________________________________________
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