Minimum Spanning Tree
Actually,
library(igraph)
tab <- read.csv("http://www.nabble.com/file/p22957493/sp_matrix.csv")
tab <- tab[,-1]
g <- graph.adjacency(as.matrix(tab), weighted=TRUE)
V(g)$label <- V(g)$name
mst <- as.undirected(minimum.spanning.tree(g))
lay <- layout.reingold.tilford(mst, root=which.max(degree(mst))-1)
lay <- cbind(lay[,2], lay[,1]) # rotate
x11(width=15, height=8)
plot(mst, layout=lay, vertex.size=25, vertex.size2=10,
vertex.shape="rectangle", asp=FALSE,
vertex.label.cex=0.7, vertex.color="white")
works relatively well for me on your graph. It doesn't for you?
Best,
Gabor
On Wed, Apr 8, 2009 at 9:14 PM, jpearl01 <joshearl1 at hotmail.com> wrote:
Make the graph undirected first and then choose the right plotting parameters. E.g. the following works fine for me: set.seed(2) g <- erdos.renyi.game(100, 300, type="gnm", directed=TRUE) E(g)$weight <- runif(ecount(g)) mst <- minimum.spanning.tree(g) mst <- simplify(as.undirected(mst)) lay <- layout.reingold.tilford(mst, root=which.max(degree(mst))-1) plot(mst, layout=lay, vertex.size=5, asp=FALSE, vertex.color=NA, ? ? ? vertex.frame.color=NA) G. Thanks for all your help Gabor, ?However, I'm unable to get a display in R which is at all readable. ?I'm not sure why that is (if the data is generated randomly, like in your example the tree builds/reads fine... however on my dataset whichever node is picked as the root just completely over powers the rest of the nodes which all clump together in a manner that is unreadable). ?My dataset is: http://www.nabble.com/file/p22957493/sp_matrix.csv sp_matrix.csv If you would like to take a look. ?However, as it stands I think I'll have to find another option. ?Thanks again for all your efforts. ~josh -- View this message in context: http://www.nabble.com/Minimum-Spanning-Tree-tp22934813p22957493.html Sent from the R help mailing list archive at Nabble.com.
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Gabor Csardi <Gabor.Csardi at unil.ch> UNIL DGM