Thursday, March 2, 2017

Function to plot a tree with error bars on divergence dates in R

Yesterday I posted about plotting error bars around divergence times onto internal nodes of the tree.

The following (plotTree.errorbars) is a function to automate this procedure, to be shortly added to phytools.

## plot tree with error bars around divergence times at nodes
## written by Liam J. Revell 2017
plotTree.errorbars<-function(tree,CI,...){
    args<-list(...)
    if(!is.null(args$gridlines)){ 
        gridlines<-args$gridlines
        args$gridlines<-NULL
    } else gridlines<-TRUE
    if(is.null(args$mar)) args$mar<-c(4.1,1.1,1.1,1.1)
    if(is.null(args$ftype)) args$ftype<-"i"
    fsize<-if(!is.null(args$fsize)) args$fsize else 1
    if(is.null(args$direction)) args$direction<-"leftwards"
    if(!is.null(args$bar.width)){
        bar.width<-args$bar.width
        args$bar.width<-NULL
    } else bar.width<-11
    if(!is.null(args$cex)){
        cex<-args$cex
        args$cex<-NULL
    } else cex<-1.2
    if(!is.null(args$bar.col)){
        bar.col<-args$bar.col
        args$bar.col<-NULL
    } else bar.col<-"blue"
    par(mar=args$mar)
    plot.new()      
    th<-max(nodeHeights(tree))
    h<-max(th,max(CI))
    if(is.null(args$xlim)){
        m<-min(min(nodeHeights(tree)),min(CI))
        d<-diff(c(m,h))
        pp<-par("pin")[1]
        sw<-fsize*(max(strwidth(tree$tip.label,units="inches")))+
            1.37*fsize*strwidth("W",units="inches")
        alp<-optimize(function(a,d,sw,pp) (a*1.04*d+sw-pp)^2,
            d=d,sw=sw,pp=pp,
            interval=c(0,1e6))$minimum
        args$xlim<-if(args$direction=="leftwards") c(h,m-sw/alp) else 
            c(m,h+sw/alp)
    }
    if(is.null(args$at)) at<-seq(0,h,by=h/5)
    else {
        at<-args$at
        args$at<-NULL
    }
    args$tree<-tree
    args$add<-TRUE
    do.call(plotTree,args=args)
    if(gridlines) abline(v=at,lty="dashed",
        col=make.transparent("grey",0.5))
    axis(1,at=at,labels=signif(at,3))
    obj<-get("last_plot.phylo",envir=.PlotPhyloEnv)
    for(i in 1:tree$Nnode+Ntip(tree))
        lines(x=c(CI[i-Ntip(tree),1],CI[i-Ntip(tree),2]),
            y=rep(obj$yy[i],2),lwd=bar.width,lend=0,
            col=make.transparent(bar.col,0.4))
    points(obj$xx[1:tree$Nnode+Ntip(tree)],
        obj$yy[1:tree$Nnode+Ntip(tree)],pch=19,col=bar.col,
        cex=cex)
}

As I have mentioned in an earlier post - one of the most difficult components of plotting a tree in R is leaving enough space in the plotting window for the tip labels. This is because we normally don't know how much space a particular string will occupy (in user units) until we have already opened our plotting device & set our xlim and ylim values. Consequently, the example will use a tree with tip labels B through Z, plus one really long tip label, to make sure that enough space has been allocated. BTW, my solution to this problem (above) is adapted from plot.phylo in the ape package.

OK, now let's test it out:

library(phytools)
tree
## 
## Phylogenetic tree with 26 tips and 25 internal nodes.
## 
## Tip labels:
##  Z, Y, X, W, V, U, ...
## 
## Rooted; includes branch lengths.
CI
##        lower     upper
## 27 2.8414221 2.2855101
## 28 2.4025799 1.7851208
## 29 1.1518398 0.6932472
## 30 1.1016629 0.5915718
## 31 1.5786906 0.9097206
## 32 1.2866289 0.6838407
## 33 0.4025250 0.0000000
## 34 0.7735031 0.2052436
## 35 0.6981268 0.2212514
## 36 2.7675974 2.1440829
## 37 2.3925982 1.8320681
## 38 1.5706797 0.9821414
## 39 1.2980457 0.9041184
## 40 1.1321683 0.5452341
## 41 0.4097613 0.0000000
## 42 0.4676039 0.0000000
## 43 0.7283202 0.2276139
## 44 0.4388847 0.0000000
## 45 1.2948954 0.7909557
## 46 0.6314838 0.1167126
## 47 1.2049871 0.6604358
## 48 1.0396180 0.5733247
## 49 0.5778952 0.1890986
## 50 0.3843571 0.0000000
## 51 1.0729443 0.5512091
plotTree.errorbars(tree,CI)

plot of chunk unnamed-chunk-2

Note that there is a lot we can do to modify this plot. Firstly, any argument of plotTree can be passed internally to that function. For instance:

plotTree.errorbars(tree,CI,lwd=5,color="navy",lend=0)

plot of chunk unnamed-chunk-3

However, it is also possible to modify the specify attributes of the plot. For instance:

plotTree.errorbars(tree,CI,lwd=1,bar.col="red",bar.width=7,cex=1,
    at=seq(0,3,by=0.5))

plot of chunk unnamed-chunk-4

Pretty neat.

The tree & CIs for this example were simulated as follows:

tree<-pbtree(n=26,tip.label=LETTERS[26:1])
tree$tip.label[26]<-"Some really long tip label."
h<-sapply(1:tree$Nnode+Ntip(tree),nodeheight,tree=tree)
d<-max(nodeHeights(tree))
CI<-cbind(h-runif(n=length(h),min=.10*d,max=.20*d),h+runif(n=length(h),
    min=.05*d,max=.10*d))
CI[CI>max(nodeHeights(tree))]<-max(nodeHeights(tree))
CI<-max(nodeHeights(tree))-CI
rownames(CI)<-1:tree$Nnode+Ntip(tree)
colnames(CI)<-c("lower","upper")

No comments:

Post a Comment