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.).

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