[R] community finding in a graph and heatplot

[Gábor Csárdi]

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