[R] community finding in a graph and heatplot

[Aziz, Muhammad Fayez]

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.gabor at gmail.com [csardi.gabor at gmail.com] on behalf of Gábor Csárdi [csardi at rmki.kfki.hu]
Sent: Thursday, May 31, 2012 10:45 AM
To: Aziz, Muhammad Fayez
Cc: r-help at 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
<aziz4 at 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]]
>
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--
Gabor Csardi <csardi at rmki.kfki.hu>     MTA KFKI RMKI