Wednesday, April 26, 2017

Complete re-write of phytools densityTree function (& many new options)

Earlier today I posted about plotting multiple trees with conflicting topologies in the same plotting device.

There is theoretically a function in phytools called densityTree that automates at least some of these options; however in the process of preparing this post I discovered that the function appears to be a little bit broken.

In particular, this is what we get when we apply densityTree to the 9 trees from our previous example:

library(phytools)
trees
## 9 phylogenetic trees
densityTree(trees)

plot of chunk unnamed-chunk-1

Oops! That's no good.

Anyhow, I'm going to try & fix that as well as add some additional features to the function, and in so doing I intend to employ some of the tricks that I used in today's post.

Here is the re-written function:

## function to be used internally
rescaleTree<-function(tree,scale){
    tree$edge.length<-tree$edge.length/max(nodeHeights(tree))*scale
    tree
}
## densityTree function
densityTree<-function(trees,colors="blue",alpha=NULL,method="plotTree",
    fix.depth=FALSE,use.edge.length=TRUE,compute.consensus=TRUE,
    use.gradient=FALSE,show.axis=TRUE,...){
    N<-length(trees)
    if(any(sapply(trees,function(x) is.null(x$edge.length)))) 
        use.edge.length<-FALSE
    if(!use.edge.length) trees<-lapply(trees,compute.brlen)
    h<-sapply(trees,function(x) max(nodeHeights(x)))
    if(fix.depth){
        if(method=="plotTree"){
            trees<-lapply(trees,rescaleTree,mean(h))
            class(trees)<-"multiPhylo"
        } else if(method=="plotSimmap"){ 
            trees<-rescaleSimmap(trees,depth=mean(h))
            print(class(trees))
            print(class(trees[[1]]))
        }
        h<-sapply(trees,function(x) max(nodeHeights(x)))
    }
    tips<-setNames(1:Ntip(trees[[1]]), 
        if(compute.consensus) untangle(consensus(trees),
            "read.tree")$tip.label 
        else trees[[1]]$tip.label)
    if(is.null(alpha)) alpha<-max(c(1/N,0.01))
    args<-list(...)
    args$direction<-"leftwards"
    args$tips<-tips
    args$add<-FALSE
    if(is.null(args$nodes)) args$nodes<-"inner"
    if(is.null(args$mar)) args$mar<-if(show.axis) c(4.1,1.1,1.1,1.1) else rep(1.1,4)
    if(is.null(args$ftype)) args$ftype<-"i"
    if(!use.gradient){
        plotTree(trees[[which(h==max(h))[1]]],direction="leftwards",mar=args$mar,
            plot=FALSE)
        args$xlim<-get("last_plot.phylo",envir=.PlotPhyloEnv)$x.lim[2:1]
        if(method=="plotTree"){
            args$color<-make.transparent(colors[1],alpha)
            for(i in 1:length(trees)){
                args$tree<-trees[[i]]
                do.call(plotTree,args)
                if(i==1){ 
                    if(show.axis) axis(1)
                    args$ftype<-"off"
                    args$add<-TRUE
                }
            }
        } else if(method=="plotSimmap"){
            states<-sort(unique(as.vector(mapped.states(trees))))
            print(states)
            print(colors)
            if(length(colors)!=length(states)){
                colors<-setNames(c("grey",palette()[2:length(states)]),
                    states)
            }
            colors<-sapply(colors,make.transparent,alpha=alpha)
            args$colors<-colors
            for(i in 1:length(trees)){
                args$tree<-trees[[i]]
                do.call(plotSimmap,args)
                if(i==1){ 
                    if(show.axis) axis(1)
                    args$ftype<-"off"
                    args$add<-TRUE
                }
            }
        }
    } else if(use.gradient){
        nulo<-capture.output(rf<-multiRF(trees),type="message")
        mds<-cmdscale(rf,k=1)[,1]
        trees<-trees[order(mds)]
        args$ylim<-c(0,Ntip(trees[[1]])+1)
        plotTree(trees[[which(h==max(h))[1]]],direction="leftwards",mar=args$mar,
            ylim=args$ylim,plot=FALSE)
        args$xlim<-get("last_plot.phylo",envir=.PlotPhyloEnv)$x.lim[2:1]
        colors<-sapply(rainbow(n=length(trees)),make.transparent,alpha=alpha)
        ftype<-args$ftype
        for(i in 1:length(trees)){
            y.shift<-(i-median(1:length(trees)))/length(trees)/2
            args$tree<-trees[[i]]
            args$tips<-tips+y.shift
            args$color<-colors[i]
            args$ftype<-if(i==floor(median(1:length(trees)))) ftype else "off"
            do.call(plotTree,args)
            if(i==1){ 
                if(show.axis) axis(1)
                args$ftype<-"off"
                args$add<-TRUE
            }
        }
    }
}

We can try it out using various options. Note, to follow along you will have to update phytools from GitHub.

First, the basic method:

densityTree(trees)

plot of chunk unnamed-chunk-3

or fix the total depth to be a constant value:

densityTree(trees,color="red",fix.depth=TRUE)

plot of chunk unnamed-chunk-4

We can also use a color gradient to be able to better distinguish the different topologies. I demonstrated this option today. I also added the feature that the method first sorts the trees (in a way) by computing the Robinson-Foulds distances between topologies & the uses MDS to sort the trees into one dimension. That means that plotted trees with similar gradient colors tend to have more similar topologies!

densityTree(trees,use.gradient=TRUE,fix.depth=TRUE,alpha=0.2)
## Some trees are rooted. Unrooting all trees.

plot of chunk unnamed-chunk-5

This function also allows a mapped discrete character by changing the argument method to plotSimmap. Let's try it:

mtrees
## 90 phylogenetic trees with mapped discrete characters
densityTree(mtrees,colors=setNames(c("blue","red"),letters[1:2]),method="plotSimmap",
    nodes="intermediate")

plot of chunk unnamed-chunk-6

Lastly, let's try it on a larger set of slightly bigger trees to see how it works:

tt
## 99 phylogenetic trees
densityTree(tt)

plot of chunk unnamed-chunk-7

densityTree(tt,use.gradient=TRUE,alpha=0.05,fix.depth=TRUE)
## Some trees are rooted. Unrooting all trees.

plot of chunk unnamed-chunk-8

Cool.

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