A phytools user recently wrote in to ask if she could color the terminal
edges of a phylogeny plotted using `plotTree.wBars`

different
colors depending on a discrete trait. Well, we
already
know that it's possible to plot a tree with a mapped discrete character.
So to accomplish this, we just need to paint the terminal edges of the tree
using the phytools function `paintSubTree`

.

Here's a demo using simulated data:

```
library(phytools)
## let's simulate a tree & some data
tree<-pbtree(n=100,scale=1)
x<-fastBM(tree)
x<-x-min(x) ## set min to zero
th<-setNames(c(max(x)/4*1:3,Inf),LETTERS[1:4])
y<-sapply(x,threshState,th)
y
```

```
## t71 t72 t59 t2 t29 t99 t100 t70 t81 t82 t20 t21 t22 t23 t53
## "B" "B" "C" "B" "C" "D" "D" "A" "A" "A" "B" "C" "D" "D" "C"
## t54 t65 t66 t14 t15 t10 t6 t16 t79 t80 t40 t8 t9 t1 t17
## "C" "B" "A" "A" "B" "B" "B" "C" "C" "C" "B" "B" "B" "B" "C"
## t93 t94 t37 t63 t64 t32 t3 t48 t89 t90 t43 t44 t67 t68 t91
## "C" "C" "B" "B" "B" "B" "B" "B" "B" "B" "D" "C" "C" "B" "B"
## t92 t38 t11 t12 t13 t30 t31 t7 t57 t58 t45 t75 t78 t95 t96
## "B" "B" "B" "C" "C" "B" "A" "C" "B" "B" "B" "B" "B" "B" "B"
## t60 t61 t62 t33 t34 t73 t74 t76 t77 t51 t55 t56 t18 t49 t50
## "B" "C" "C" "C" "C" "B" "B" "C" "B" "C" "C" "C" "B" "C" "C"
## t35 t85 t86 t36 t46 t47 t19 t4 t27 t28 t52 t83 t84 t87 t88
## "B" "B" "B" "B" "A" "A" "A" "A" "B" "B" "B" "B" "B" "B" "B"
## t39 t25 t26 t24 t97 t98 t69 t41 t42 t5
## "B" "B" "A" "A" "B" "B" "B" "C" "D" "C"
```

OK, so now we have data approximating the empirical data and we can attempt to
generate our simulation. We will do this by first coloring all the terminal
edges of the tree according to our discrete character, and then, having done
that, we will run `plotTree.wBars`

using the `method="plotSimmap"`

.

```
## first color the tip edges
for(i in 1:length(y)) tree<-paintSubTree(tree,node=i,state=y[i],stem=TRUE)
colors<-setNames(c("black","red","blue","green","orange"),c(1,LETTERS[1:4]))
plotSimmap(tree,type="fan",colors=colors)
```

```
## setEnv=TRUE for this type is experimental. please be patient with bugs
```

```
add.simmap.legend(colors=colors[2:5],prompt=FALSE,x=0.95*par()$usr[1],y=0.95*par()$usr[4])
```

```
## now plot with bars
plotTree.wBars(tree,x,method="plotSimmap",colors=colors,type="fan",scale=0.1)
add.simmap.legend(colors=colors[2:5],prompt=FALSE,x=0.95*par()$usr[1],y=0.95*par()$usr[4])
```

Obviously, the user will have to vary this to get the desired plot for their own data, but this is the general idea!