Superb. It works. The results loo great. I just tweaked the function a little
bit to suit my needs though. I passed merges and vcount separately as
fgc$merges and vcount(g). The vcount attribute was not there in fgc object.
Also, I removed the last row from the merges matrix before returning as it was
adding the very root level undesired by the heatmap.2 function I was using. The
final function looks like this:
# To generate a complete dendogram from disconnected subgraphs in merges given
by fgc
complete.dend <- function(merges, vcount) {
if (nrow(merges) < vcount-1) {
miss <- seq_len(vcount + nrow(merges))[-as.vector(merges)]
miss <- c(miss, seq_len(length(miss)-2) + vcount+nrow(merges))
miss <- matrix(miss, byrow=TRUE, ncol=2)
merges <- rbind(merges, miss)
}
storage.mode(merges) <- "integer"
merges[-nrow(merges),] # skip last row
}
Thank you so much Gabor for this custom complete.dend fucntion. I couldn't find
it in the regular igraph library
(http://igraph.sourceforge.net/doc/R/00Index.html).
Best,
Fayez
________________________________________
From: csardi.ga...@gmail.com [csardi.ga...@gmail.com] on behalf of Gábor Csárdi
[csa...@rmki.kfki.hu]
Sent: Monday, June 04, 2012 6:33 PM
To: Aziz, Muhammad Fayez
Cc: r-help@r-project.org; Caetano-Anolles, Gustavo
Subject: Re: [R] community finding in a graph and heatplot
On Sun, Jun 3, 2012 at 4:11 PM, Aziz, Muhammad Fayez <az...@illinois.edu> wrote:
>
> Hmm interesting. To come to think of it there could be many disconnected
> components in the graph and thus there should be a generic way to either
> mitigate the disconnectedness in the dendrogram or in the original graph. I
> had no luck in finding such a trick though google search. I then ran the
> script on minute-scale graphs and have following results:
>
> 1) disconnected graph with three modules:
>
> *Vertices 9
> *Edges
> 1 2 1
> 2 3 1
> 3 1 1
> 4 5 1
> 5 6 1
> 6 4 1
> 7 8 1
> 8 9 1
> 9 7 1
>
> corresponding fgc$merges matrix:
>
> [,1] [,2]
> [1,] 1 0
> [2,] 2 9
> [3,] 7 6
> [4,] 8 11
> [5,] 4 3
> [6,] 5 13
>
> 2) connected graph by adding links 1-2 and 4-7 in graph 1):
>
> *Vertices 9
> *Edges
> 1 2 1
> 2 3 1
> 3 1 1
> 4 5 1
> 5 6 1
> 6 4 1
> 7 8 1
> 8 9 1
> 9 7 1
> 1 4 1
> 4 7 1
>
> corresponding fgc$merges matrix:
>
> [,1] [,2]
> [1,] 2 1
> [2,] 0 9
> [3,] 8 7
> [4,] 6 11
> [5,] 5 4
> [6,] 3 13
> [7,] 14 12
> [8,] 15 10
>
> There needs to be a generic way to get fgc$merges of the form 2) from 1).
> Hints please.
Well, how do you merge the unconnected components? I guess you could
come up with an order based on modularity, or just merge them in
arbitrary order. The following is from igraph 0.6, and I haven't tried
it on your data, but it might just work. It merges the individual
subtrees in arbitrary order.
complete.dend <- function(comm) {
merges <- comm$merges
if (nrow(merges) < comm$vcount-1) {
miss <- seq_len(comm$vcount + nrow(merges))[-as.vector(merges)]
miss <- c(miss, seq_len(length(miss)-2) + comm$vcount+nrow(merges))
miss <- matrix(miss, byrow=TRUE, ncol=2)
merges <- rbind(merges, miss)
}
storage.mode(merges) <- "integer"
merges
}
Best,
Gabor
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