I recently saw a
post describing how
to plot a tree with colored boxes around tip labels using the neat package
*ggtree*.

Of course, it is also straightforward to do this using R base graphics. The following is just one example of how to do that:

```
library(phytools)
## custom function I'm going to use for the box labels
boxlabel<-function(x,y,text,cex=1,bg="transparent",offset=0){
w<-strwidth(text)*cex*1.1
h<-strheight(text)*cex*1.4
os<-offset*strwidth("W")*cex
rect(x+os,y-0.5*h,x+w+os,y+0.5*h,col=bg,border=0)
text(x,y,text,pos=4,offset=offset,font=3)
}
## our tree
tree
```

```
##
## Phylogenetic tree with 26 tips and 25 internal nodes.
##
## Tip labels:
## M.tlxdfmsc, Y.fnblkxm, T.njirxywqec, D.brdqgfkwz, A.cmegtpxbjn, P.gdpbcqm, ...
##
## Rooted; includes branch lengths.
```

```
## our character for the colors:
x
```

```
## M.tlxdfmsc Y.fnblkxm T.njirxywqec D.brdqgfkwz A.cmegtpxbjn
## c b b b a
## P.gdpbcqm R.pyjxbva N.brklwqft G.opbufyimec K.atmhkx
## b b a c b
## C.oithaf V.zmplhwtjcs F.ualphzk Z.iwghoftx L.myxblzdj
## c a a b a
## S.cxmvdgeuy W.lpsafhe E.zaxwcnjq I.kavmis B.pxiwkbzum
## a a c c c
## X.zoabkhc Q.wyhvmegitz H.cjrunxewak U.nuxeic O.kcwyhl
## c c b b c
## J.ytcumhoagw
## b
## Levels: a b c
```

```
## our colors:
cols<-setNames(RColorBrewer::brewer.pal(length(unique(x)),"Accent"),sort(unique(x)))
cols
```

```
## a b c
## "#7FC97F" "#BEAED4" "#FDC086"
```

```
## now our plot:
par(fg="transparent")
plotTree(tree)
pp<-get("last_plot.phylo",envir=.PlotPhyloEnv)
N<-Ntip(tree)
par(fg="black")
for(i in 1:Ntip(tree)) boxlabel(pp$xx[i],pp$yy[i],tree$tip.label[i],bg=cols[x[i]])
```

Of course, if the colors for the tip data come from a character purported to have evolved on the tree, perhaps we want to also show a stochastic character map of the same character evolving up the tree as follows:

```
par(fg="transparent")
plot(make.simmap(tree,x),cols,lwd=4)
```

```
## make.simmap is sampling character histories conditioned on the transition matrix
##
## Q =
## a b c
## a -0.5411151 0.5411151 0.0000000
## b 0.5411151 -1.2691823 0.7280672
## c 0.0000000 0.7280672 -0.7280672
## (estimated using likelihood);
## and (mean) root node prior probabilities
## pi =
## a b c
## 0.3333333 0.3333333 0.3333333
```

```
## Done.
```

```
par(fg="black")
for(i in 1:Ntip(tree)) boxlabel(pp$xx[i],pp$yy[i],tree$tip.label[i],bg=cols[x[i]])
add.simmap.legend(colors=cols,prompt=F,x=5.7,y=26,fsize=2,shape="circle")
```

Or maybe we want to show posterior probabilities at nodes of the tree from a set of stochastic maps:

```
trees<-make.simmap(tree,x,nsim=100)
```

```
## make.simmap is sampling character histories conditioned on the transition matrix
##
## Q =
## a b c
## a -0.5411151 0.5411151 0.0000000
## b 0.5411151 -1.2691823 0.7280672
## c 0.0000000 0.7280672 -0.7280672
## (estimated using likelihood);
## and (mean) root node prior probabilities
## pi =
## a b c
## 0.3333333 0.3333333 0.3333333
```

```
## Done.
```

```
par(fg="transparent")
plot(trees[[1]],cols,lwd=4)
nodelabels(pie=summary(trees)$ace,piecol=cols,cex=0.8)
par(fg="black")
for(i in 1:Ntip(tree)) boxlabel(pp$xx[i],pp$yy[i],tree$tip.label[i],bg=cols[x[i]])
add.simmap.legend(colors=cols,prompt=F,x=5.7,y=26,fsize=2,shape="circle")
```

That's pretty neat too.

The tree & data were simulated (to have realistic looking tip labels) as follows:

```
tree<-rtree(26,tip.label=LETTERS)
for(i in 1:Ntip(tree))
tree$tip.label[i]<-paste(tree$tip.label[i],".",paste(sample(letters,sample(6:10,1)),
collapse=""),sep="")
Q<-matrix(c(-1,1,0,1,-2,1,0,1,-1),3,3,dimnames=list(letters[1:3],letters[1:3]))
x<-as.factor(sim.history(tree,Q)$states)
```

Unfortunately, the size of the boxes does not scale automatically with the size of the tree and it looks poor with different output formats (png, pdf, etc.).

ReplyDeleteYes, it is completely customizable - but, like many things in R, that customizability needs to be done manually by the user. Let me know what you don't like & I'd be happy to help you get it right.

DeleteR does not export to PNG very well, but when I export to PDF it looks great!

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ReplyDelete