search for: nodelabels

Is there a way to DRY this up a bit? named_scope :has_valid_sysoid, lambda{|sysoid| (sysoid.nil?) ? {:conditions => ["nodesysoid IS NOT NULL AND nodelabel LIKE ''%-to-%''"], :include => [:ipinterface, :alarm]} : {:conditions => ["nodesysoid IS NOT NULL AND nodelabel LIKE ''%-to-%'' AND nodesysoid = ? ", sysoid], :include =>

Hi, I've been investigating the ape package for a while, and I was wondering if it is possible to: - display the names of the internal nodes (from a newick tree) - plot a pie-chart on top of each of the internal branches in a phylogram plot Thanks in advance, Cheers, Albert.

...e = "clustal.tre", sep = "\n") clustal.tree4 <- read.tree("clustal.tre") plot(clustal.tree4, type="unrooted", no.margin=TRUE, font=c(1,1,3,1,1,1,1,1,1)) unlink("clustal.tre") text.lab < -c(99.2,99.0,87.8,100.0,99.8,98.4) node.lab <- c(3:8) nodelabels(text=text.lab, node=node.lab, cex=.7) Any help or general suggestions are greatly appreciated, Thanks, Jerry Graduate Student, Missouri State University R 2.2.0 Windows XP

...mentioned here: http://www.mail-archive.com/r-sig-phylo at r-project.org/msg00537.html An example: library(ape) set.seed(5) x <- matrix(rnorm(100), ncol=10) p <- as.phylo(hclust(dist(x))) p.new <- extract.clade(p, 14) par(mfcol=c(1,2), mar=c(1,1,5,1)) plot(p) title('original') nodelabels() plot(p.new) title('cut at node 14') I have noticed that this error is present only sometimes... i.e. when I use a different seed for the random matrix 'x', the results are correct in some cases. Any ideas? Thanks for the very useful 'ape' package! Cheers, Dylan...

...ree$node.label<-pr #labels the nodes with the character states write.tree(tree, file="T")#exports tree with nodes character states to directory #configuration in figtree - node label display label #tree pie charts pdf("TREE_PLOT.pdf", height=11, width=8.5) plot(tree ,cex=.8) nodelabels(pie=pie.probs,piecol=c("blue","red","yellow"), cex=.5) dev.off() [[alternative HTML version deleted]]

Dear all, I'm using the "ape" package in R and want to draw a phylogenetic tree with not only the tip labels but also some labels for the edges. e.g. Mark the edge AB as "m" in the tree ABC. Couldn't find a way to do that. Can someone help? Thanks, Hua