[R] Nodes & edges with similarity matrix
csardi at rmki.kfki.hu
Tue Aug 28 23:44:58 CEST 2007
i have no idea what functionality you need from graph, but
if the igraph package can do what you want then it can
easily convert this to a graph for you, basically it is just
threshold <- 0.5
g <- graph.adjacency(sim>threshoold)
or you can create a weighted graph:
g <- graph.adjacency(sim, weighted=TRUE)
or a weighted graph after a threshold:
sim2 <- sim
sim2[ sim<threshold ] <- 0
g <- graph.adjacency(sim2, weighted=TRUE)
On Tue, Aug 28, 2007 at 02:25:27PM -0700, H. Paul Benton wrote:
> I apologise if someone has already answered this but I searched and
> googled but didn't find anything.
> I have a matrix which gives me the similarity of each item to each
> other. I would like to turn this matrix into something like what they
> have in the graph package with the nodes and edges.
> http://cran.r-project.org/doc/packages/graph.pdf . However I cannot find
> a method to convert my matrix to an object that graph can use.
> my similarity matrix looks like:
> > sim[1:4,]
> a b c d
> [a] 1.000000000 0.0223676 0.9723831 0.3943310
> [b] 0.325141612 1.0000000 0.9644216 0.5460461
> [c] 0.002109751 0.3426540 1.0000000 0.7080224
> [d] 0.250153137 0.1987485 0.7391222 1.0000000
> please don't get caught up with the numbers I simple made this to show.
> I have not produce the code yet to make my similitary matrix.
> Does anyone know a method to do this or do I have to write something. :(
> If I do any starter code :D jj. If I've read something wrong or
> misunderstood my apologies.
> Research Technician
> Mass Spectrometry
> o The
> o Scripps
> o Research
> o Institute
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Csardi Gabor <csardi at rmki.kfki.hu> MTA RMKI, ELTE TTK
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