R help - May 2012 - community finding in a graph and heatplot

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. 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]]

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