Generating a ggplot phylomorphospace plot with phytools

Today a colleague & phytools user, Werner de Gier, tweeted the following about using phytools to graph a phylomorphospace projection with ggplot2.

Hey! Maybe it's common knowledge already, but I found that the "path" the phylomorphospace made is stored in the function in phytools. So if obj <- phylomorphospace(), than the coordinates are saved as $xx and $yy, and the path from node to node is saved as $edge. (½)

— Werner de Gier (@Werner_deGier) December 14, 2022

My reaction was the following.

Why, though?

JK. If you want to send me your ggplot::geom_segment R code, I'd be happy to throw it up on my blog as a demo (assuming I can replicate it without Excel).

FWIW, something similar is also possible for ANY plotted tree from phytools....

— Liam Revell (@phytools_liam) December 14, 2022

I nonetheless promised to share his solution on this blog – assuming that I could get it to work without the Microsoft Excel step!

Here it is.

First, let’s load our libraries.

library(phytools)
library(ggplot2)

Now let’s pull in our data.

These come from Revell & Collar (2009).

data(sunfish.tree)
tree<-as.phylo(sunfish.tree)
plotTree(tree,ftype="i",fsize=0.8)

data(sunfish.data)
head(sunfish.data)

##                      feeding.mode gape.width buccal.length
## Acantharchus_pomotis         pisc      0.114        -0.009
## Lepomis_gibbosus              non     -0.133        -0.009
## Lepomis_microlophus           non     -0.151         0.012
## Lepomis_punctatus             non     -0.103        -0.019
## Lepomis_miniatus              non     -0.134         0.001
## Lepomis_auritus               non     -0.222        -0.039

X<-sunfish.data[,2:3]

Now let’s create a phylomorphospace projection using phytools.

obj<-phylomorphospace(tree,X,ftype="off",bty="n",node.size=c(0,1.2))
grid()

As Werner pointed out, phylomorphospace returns the phylomorphospace coordinates to the user invisibly. Let’s use them to create a data frame to be passed to ggplot2::geom_segment.

Data<-data.frame(
	xstart=obj$xx[obj$edge[,1]],
	ystart=obj$yy[obj$edge[,1]],
	xstop=obj$xx[obj$edge[,2]],
	ystop=obj$yy[obj$edge[,2]],
	nodestart=obj$edge[,1],
	nodestop=obj$edge[,2])

Here’s what that looks like:

head(Data)

##         xstart       ystart       xstop        ystop nodestart nodestop
## 1   0.03520284 -0.002225660  0.11400000 -0.009000000        29        1
## 30  0.03520284 -0.002225660  0.02429463 -0.001287860        29       30
## 31  0.02429463 -0.001287860  0.01151996 -0.003347729        30       31
## 32  0.01151996 -0.003347729 -0.04908695 -0.001822143        31       32
## 33 -0.04908695 -0.001822143 -0.10899316 -0.015630236        32       33
## 34 -0.10899316 -0.015630236 -0.11776881 -0.011263323        33       34

Finally, let’s create out plot!

ggplot()+
	geom_point(data= X,aes(x=gape.width,y=buccal.length),
	size=3,color="darkblue")+
	geom_segment(data=Data,aes(x=xstart,y=ystart,xend=xstop,yend=ystop), 
	size = 1,color="darkblue")

Neat. We’re done.