Monday, February 27, 2017

Function to add error bars to a contMap plot

I just wrote a function to add error bars to a "contMap" plot, as discussed today on R-sig-phylo and my blog.

The function looks as follows:

errorbar.contMap<-function(obj,...){
    if(hasArg(x)) x<-list(...)$x
    else x<-setNames(sapply(1:Ntip(obj$tree),function(x,obj){
        ii<-which(obj$tree$edge[,2]==x)
        ss<-names(obj$tree$maps[[ii]][length(obj$tree$maps[[ii]])])
        obj$lims[1]+as.numeric(ss)/(length(obj$cols)-1)*diff(obj$lims)
        },obj=obj),obj$tree$tip.label)
    if(hasArg(scale.by.ci)) scale.by.ci<-list(...)$scale.by.ci
    else scale.by.ci<-FALSE
    tree<-obj$tree
    aa<-fastAnc(tree,x,CI=TRUE)
    xlim<-range(aa$CI95)
    if(xlim[2]>obj$lims[2]||xlim[1]<obj$lims[1]){
        cat(paste("  -----\n  The range of the contMap object, presently (",
            round(obj$lims[1],4),",",
            round(obj$lims[2],4),
            "), should be equal to\n  or greater than the range of the CIs on ancestral states: (",
            round(xlim[1],4),",",round(xlim[2],4),").\n",sep=""))
        cat(paste("  To ensure that your error bars are correctly plotted, please recompute your\n", 
            "  contMap object and increase lims.\n  -----\n",sep=""))
    }
    d<-diff(obj$lims)
    if(scale.by.ci){
        v<-aa$CI95[,2]-aa$CI95[,1]
        v<-v/max(v)
    } else v<-rep(0.5,tree$Nnode)
    n<-length(obj$cols)-1
    lastPP<-get("last_plot.phylo",envir=.PlotPhyloEnv)
    h<-max(nodeHeights(tree))
    for(i in 1:tree$Nnode){
        ii<-round((aa$CI95[i,1]-obj$lims[1])/d*n)
        jj<-round((aa$CI95[i,2]-obj$lims[1])/d*(n+1))
        cols<-obj$cols[ii:jj]   
        add.color.bar(leg=0.1*h*v[i],cols=cols,prompt=FALSE,
            x=lastPP$xx[i+Ntip(tree)]-0.05*h*v[i],
            y=lastPP$yy[i+Ntip(tree)],title="",subtitle="",lims=NULL,
            lwd=14)
    }
}

One element of the function

x<-setNames(sapply(1:Ntip(obj$tree),function(x,obj){
    ii<-which(obj$tree$edge[,2]==x)
    ss<-names(obj$tree$maps[[ii]][length(obj$tree$maps[[ii]])])
    obj$lims[1]+as.numeric(ss)/(length(obj$cols)-1)*diff(obj$lims)
    },obj=obj),obj$tree$tip.label)

is a complicated piece of code that is only used if the optional argument x (the same as x in contMap is not supplied. What this line does is pull the values of x instead from the mapped object.

OK, let's try it:

library(phytools)
tree
## 
## Phylogenetic tree with 26 tips and 25 internal nodes.
## 
## Tip labels:
##  A, B, C, D, E, F, ...
## 
## Rooted; includes branch lengths.
x
##           A           B           C           D           E           F 
##  2.40577324 -2.09590799 -0.03881523 -0.32857686 -1.71533031 -1.07523748 
##           G           H           I           J           K           L 
## -0.99890853  3.07436198  4.00842163 -0.27299915  2.41135389  2.61494639 
##           M           N           O           P           Q           R 
##  2.97710788  3.56872630  2.96244691  1.92234400  3.85672218  5.70984852 
##           S           T           U           V           W           X 
##  0.15119803  0.50825014  3.26386662  2.21301397  1.52734360  1.93244087 
##           Y           Z 
##  1.51311417  4.41672993
y
##           A           B           C           D           E           F 
## -0.52075890 -3.22896754 -1.99922219 -2.99064026 -3.85137945  0.92981725 
##           G           H           I           J           K           L 
## -1.77583525 -5.53973459 -1.39568877 -6.03400572 -5.50545828 -2.04112670 
##           M           N           O           P           Q           R 
## -3.45201728 -2.87475079 -4.97170923 -1.41198149 -1.58924448  0.07361102 
##           S           T           U           V           W           X 
## -0.37121255  1.66386064  0.38763598 -3.65979548 -2.99468975 -1.57039289 
##           Y           Z 
## -0.27934165  0.97554201

First with x:

obj<-contMap(tree,x,plot=FALSE)
plot(obj,xlim=c(-0.5,10.5))
errorbar.contMap(obj,scale.by.ci=TRUE)

plot of chunk unnamed-chunk-4

Now with y:

obj<-contMap(tree,y,plot=FALSE)
plot(obj,xlim=c(-0.5,10.5))
errorbar.contMap(obj,scale.by.ci=TRUE)

plot of chunk unnamed-chunk-5

##   -----
##   The range of the contMap object, presently (-6.034,1.6639), should be equal to
##   or greater than the range of the CIs on ancestral states: (-5.9555,2.7099).
##   To ensure that your error bars are correctly plotted, please recompute your
##   contMap object and increase lims.
##   -----

This tells us that the range of the CIs on the ancestral nodes for y exceeds the limits of the "contMap" object. This is why some of the plotted CIs (most noticeably, the root) have black regions. This should be easy to fix as follows:

obj<-contMap(tree,y,lims=c(-6,2.8),plot=FALSE)
plot(obj,xlim=c(-0.5,10.5))
errorbar.contMap(obj,scale.by.ci=TRUE)

plot of chunk unnamed-chunk-6

Some of the kinks are still being worked out. Please pardon any bugs!

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