[R] Nodes & edges with similarity matrix
ggrothendieck at gmail.com
Wed Aug 29 07:19:15 CEST 2007
# test data
mat <- structure(c(1, 0.325141612, 0.002109751, 0.250153137, 0.0223676,
1, 0.342654, 0.1987485, 0.9723831, 0.9644216, 1, 0.7391222, 0.394331,
0.5460461, 0.7080224, 1), .Dim = c(4L, 4L), .Dimnames = list(
c("a", "b", "c", "d"), c("a", "b", "c", "d")))
# draw edges according to value
gplot(mat, edge.lwd = mat, label = rownames(mat))
# thresholding at 0.5
gplot(mat > .5, label = rownames(mat))
On 8/28/07, H. Paul Benton <hpbenton at scripps.edu> 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
> R-help at stat.math.ethz.ch mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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