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.ga...@gmail.com [csardi.ga...@gmail.com] on behalf of Gábor Csárdi [csa...@rmki.kfki.hu] Sent: Thursday, May 31, 2012 4:23 PM To: Aziz, Muhammad Fayez Cc: r-help@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 <az...@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.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 -- Gabor Csardi <csa...@rmki.kfki.hu> MTA KFKI RMKI
<<attachment: WhyNot.png>>
<<attachment: Splendid.png>>
______________________________________________ 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.