# [R] Nodes & edges with similarity matrix

Gabor Grothendieck ggrothendieck at gmail.com
Wed Aug 29 07:19:15 CEST 2007

```Try this:

# 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")))

library(sna)

# 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:
> Hello,
>
>    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.
>
> cheers,
>
>
> Paul
>
>
> --
> Research Technician
> Mass Spectrometry
>   o The
>  /
> o Scripps
>  \
>   o Research
>  /
> o Institute
>
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