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Hello I am working on a simulation that requires adding a number of random tips to multiple phylogenies: treeP <- read.nexus(file= "my file.tre") # 5K trees used to build a consensus tree (treeP is thus a multiPhylo object) NT = 30 # number of taxa in phylogeny N.dup = 3 # number of tips (duplications) I want to add to the trees sites <- sort(sample(1:NT, N.dup), decreasing=TRUE) # Random tips to duplicate dup.labels <- treeP[[1]]$tip.label[sites] treeP <- .uncompressTipLabel(treeP) # # Add duplicates to branches following a Liam Revell recipe published in his blog: # for (n in 1:length(treeP)) { for (i in 1:N.dup ) { pos <- runif(n=1)* treeP[[n]]$edge.length[which(treeP[[n]]$edge[,2]==sites[i])] edl <- runif(n=1)* treeP[[n]]$edge.length[which(treeP[[n]]$edge[,2]==sites[i])] treeP[[n]] <- bind.tip(treeP[[n]], tip.label=paste(dup.labels[i], 1, sep="."), edge.length=edl, where=sites[i], position=pos) } } # treeP<- .compressTipLabel(treeP) # Check tip labels: treeP$tip.label $tip.label [1] "S24" "S25" "S9" "S15" "S3" "S21" "S12" "S17" "S19" "S30" "S22" "S4" "S16" "S27" "S10" "S23" "S1" "S2" "S14" [20] "S6" "S8" "S26" "S29" "S13" "S20" "S7" "S28" "S18" "S5" "S11" "S18.1" "S20.1" "S16.1" When I plot any tree in treeP, S18.1, S20.1 and S16.1 appear together with S18, S20 and S16, as intended. So why are they at the end of the array above? This behaviour makes makes my life difficult because it forces me to rearrange a number of matrices to make them match this tip label order. I would appreciate if a kind soul can explain why it is that way and whether is possible to reorder the tip labels, placing each added tip together with its respective counterpart? Thanks in advance for your help. Juan Antonio --
Dr.
Juan
A. Balbuena |
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