Draw on a phylogeny edge with R

问题

I want to draw a symbol (cross) anywhere along an edge of a phylogeny with R.

Let us take that tree:

tree.mod

(((((hg19:0.0295977,macFas5:0.0351997)hg19-macFas5:0.0796862,otoGar3:0.153768)hg19-otoGar3:0.0189364,(((speTri2:0.136745,(mm10:0.0836004,rn5:0.0894755)mm10-rn5:0.221692)speTri2-mm10:0.009583,cavPor3:0.230585)speTri2-cavPor3:0.0279417,oryCun2:0.212423)speTri2-oryCun2:0.0141334)hg19-speTri2:0.0224427,((susScr3:0.127502,(camFer1:0.111428((HLbalAcu1:0.0196864,(HLphyCat1:0.0216245,(HLlipVex1:0.0178214,(turTru2:0.00660779,orcOrc1:0.00557822)turTru2-orcOrc1:0.0113362)HLlipVex1-turTru2:0.00784223)HLphyCat1-HLlipVex1:0.00385294)HLbalAcu1-HLphyCat1:0.0417511(bosTau7:0.0320796,oviAri3:0.0370855)bosTau7-oviAri3:0.0963575)HLbalAcu1-bosTau7:0.0212413)camFer1-HLbalAcu1:0.00459573)susScr3-camFer1:0.0425276,((equCab2:0.107972,(felCat5:0.0893591,(canFam3:0.0908515,((ailMel1:0.0208923,HLursMar1:0.0194161)ailMel1-HLursMar1:0.041512,(odoRosDiv1:0.0259201,lepWed1:0.0238902)odoRosDiv1-lepWed1:0.0288135)ailMel1-odoRosDiv1:0.0213261)canFam3-ailMel1:0.0207311)felCat5-canFam3:0.0501969)equCab2-felCat5:0.00485202,myoLuc2:0.169981)equCab2-myoLuc2:0.00361502)susScr3-equCab2:0.0302374)hg19-susScr3:0.0217021,(((loxAfr3:0.0821245,triMan1:0.0662932)loxAfr3-triMan1:0.0296365,echTel2:0.245195)loxAfr3-echTel2:0.0492624,dasNov3:0.159632)loxAfr3-dasNov3:0.00825218)hg19-loxAfr3;

and plot it with a symbol at the hg19 tip:

R
library(ape)
tree = read.tree("tree.mod")
plot(tree)
points( 0.172365, 1, col="red", pch=20)

that is easy for the tips: the 'x' value is the full branch length, and 'y' is 1,2,3...

but I don't see how to do it for inner nodes like for instance loxAfr3-triMan1. I have the 'x' but cannot find the 'y'...

Any input welcome!

回答1:

OK. I feel like I must be missing an easier way, but much of those code seems to be tucked away inside C functions called by the package's plotting function. Nevertheless, here are some functions in R that should be able to extract the x and y positions for particular nodes.

getphylo_x <- function(tree, node) {
    if(is.character(node)) {
        node <- which(c(tree$tip.label, tree$node.label)==node)
    }
    pi <- tree$edge[tree$edge[,2]==node, 1]
    if (length(pi)) {
        ei<-which(tree$edge[,1]==pi & tree$edge[,2]==node)
        tree$edge.length[ei] + Recall(tree, pi)
    } else {
        if(!is.null(tree$root.edge)) {
            tree$root.edge
        } else {
            0
        }
    }
}

getphylo_y <- function(tree, node) {
    if(is.character(node)) {
        node <- which(c(tree$tip.label, tree$node.label)==node)
    }
    ci <- tree$edge[tree$edge[,1]==node, 2]
    if (length(ci)==2) {
        mean(c(Recall(tree, ci[1]), Recall(tree, ci[2])))
    } else if (length(ci)==0) {
        Ntip <- length(tree$tip.label)
        which(tree$edge[tree$edge[, 2] <= Ntip, 2] == node)
    } else {
        stop(paste("error", length(ci)))
    }
}

To use them, you just pass in your tree and your node name. For example

node <- "loxAfr3-triMan1"
x <- getphylo_x(tree, node)
y <- getphylo_y(tree, node)


plot(tree)
points(x,y,pch=18, col="red", cex=2)

which produces

回答2:

Mr. Flick's answer seems to have this totally covered, but I thought I would add that the locator function while run with your tree plot open will allow you to get x,y coordinates of user specified points. Useful for things like x,y placement of a scale.

plot(tree)
locator()

It will return the x and y coordinates for all the points clicked before hitting Esc.

回答3:

Here is a solution that doesn't require custom functions.

Given the tree linked by the OP in one of their comments:

tree <- read.tree()   #file name isn't specified so ape will read what you paste in the console
((A:0.2,(B:0.1,C:0.1):0.1):0.1,((E:0.1,F:0.1):0.1,D:0.2):0.1);


plot(tree)
#Some random internal node:
node <- sample(tree$Nnode, 1) + length(tree$tip.label)  #nodes are not named in this tree
#if you want a (named) tip:
tip <- which(tree$tip.label == "A")
points(node.depth.edgelength(tree)[c(node, tip)], node.height(tree)[c(node,tip)], pch=18, col="red", cex=2)

来源：https://stackoverflow.com/questions/25624986/draw-on-a-phylogeny-edge-with-r

标签

phylogeny