[R] Converting edgelist to symmetric matrix/ plotting sparse network with lots of nodes

[Mike Marchywka]

> Date: Sat, 9 Apr 2011 14:34:28 -0700
> From: kmshafique at yahoo.com
> To: r-help at r-project.org
> Subject: [R] Converting edgelist to symmetric matrix
>
> Hi,
> I have network data in the form of a couple of edgelists containing weights in
> the format "x,y,weight" whereby x represents row header and y represents column
> header. All edgelists are based on links among 634 nodes and I need to convert
> them into a 634*634 weighted matrix.
>
>
> I searched for online help using possible keywords I know, but I could not find
> a clue how to do this in R. Any help will be appreciated.

I'd replied earlier suggesting the ncol format, I'd like to follow up on
that as I have tried with some success but maybe someone else can comment
on alternatives and suggest ideas for plotting. I have a set of nodes or states
specified by two parameters ( these are isotopes specified by proton and mass connected
by decay paths with probability of that path being its weight). 
This seems to almost work for your needs( note that I have taken out a lot of extraneous stuff
and may have dropped somethimng important LOL, also setup for Rgraphviz is not simple 
on 'dohs as i had to manually edit env variable etc) ,

library("Rgraphviz")
library("QuACN")
nxg<-read.graph("ncol.txt",format="ncol")
nn<-igraph.to.graphNEL(nxg)
aasd<-adjacencyMatrix(nn)
> str((aasd))
 num [1:2561, 1:2561] 0 100 95.8 2.7 0 0 0 0 0 0 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:2561] "17_10" "17_9" "16_9" "15_7" ...
  ..$ : chr [1:2561] "17_10" "17_9" "16_9" "15_7" ...


$ head ncol.txt
17_10 17_9 100
17_10 16_9 95.8
17_10 15_7 2.7
18_10 18_9 100
19_10 19_9 100
23_10 23_11 100
243_100 239_98 100
245_100 241_98 100
246_100 242_98 92
246_100 246_99 1


However, for my needs plotting has been a big problem. I apparently
have 2561 isotopes ( none of this has been validated yet LOL) that
are sparely connected by a few decay modes ( presumably acyclic directed
graph but DAG in searches didn't help much ). 





Any thoughts on which R classes to try to visualize this or even what I 
should be thinking about artistically? This is largely just a way to learn
R for some other things I want to do for analyzing data on wireless devices
but I am curious about this result too. 

Some of the things I did try are below,

library("Rgraphviz")
library("QuACN")
nxg<-read.graph("ncol.txt",format="ncol")
foo<-adjacencyMatrix(nxg)
?graphNEL
?NELgraph
df<-data.frame(nxg)
plot.igraph(nxg,layout=layout.svd)
rglplot.igraph(nxg,layout=layout.svd)
rglplot.igraph(nxg,layout=layout.svd)
rglplot.igraph(nxg)
tkplot.igraph(nxg)
library("tcltk")
tkplot.igraph(nxg)
tkplot(nxg)
dx<-decompose.graph(nxg)

nn<-igraph.to.graphNEL(nxg)
igraph.plotting(nxg)
library("sna")
gplot(nxg)
dx<-get.adjacency(nxg)
gplot(dx)
gplot3d(dx)
plot(nxg)
library("ElectroGraph")
eg<-electrograph(nxg)
eg<-electrograph(aasd)
plot(eg)




Thanks.




>
> Best regards,
> Shafique
>