[R] community finding in a graph and heatplot

[Aziz, Muhammad Fayez]

Thank you so much Gabor for taking this on. Please find attached a sample scenario with the problem of malfunctioning dendogram by fgc. I hope this helps you narrow down to the solution.

Best,
Fayez

________________________________________
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 4:23 PM
To: Aziz, Muhammad Fayez
Cc: r-help at r-project.org
Subject: Re: [R] community finding in a graph and heatplot

On Thu, May 31, 2012 at 12:08 PM, Aziz, Muhammad Fayez
<aziz4 at illinois.edu> wrote:
>
> 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?

I would need to see fgc for this. Can you send it to me in private? Or
send some self-contained example that generates the same error?

Gabor

> 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]]
>>
>> ______________________________________________
>> R-help at 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 <csardi at rmki.kfki.hu>     MTA KFKI RMKI



--
Gabor Csardi <csardi at rmki.kfki.hu>     MTA KFKI RMKI
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