Hi all I have been plotting some pruned trees recently, and have run into a problem using drop.tip() after ladderize(). If you ladderize() and then drop tips from the ladderized tree, then at least in my case the node labels are no longer correct. This may be an unlikely sequence of commands, but I thought I'd post this in case it is an easy fix, or it helps anyone else avoid issues. Thanks!
Rebecca ## require(ape) #read tree mytree<-read.tree() ((D,(E,G)1)1,((H,J)0.8,(K,(((L,M)0.5,(N,O)0.6)1,(P,(Q,R)1)1)0.7)1)1); #ladderize tree mytree.lad<-ladderize(mytree) #node labels display on both trees correctly plot(mytree,show.node.label=TRUE) plot(mytree.lad,show.node.label=TRUE) #drop tips from both trees drop.mytree<-drop.tip(mytree,c("L","D","G")) drop.mytree.lad<-drop.tip(mytree.lad,c("L","D","G")) #plot both trees, node labels are incorrect for ladderized tree plot(drop.mytree,show.node.label=TRUE) plot(drop.mytree.lad,show.node.label=TRUE) _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo