More on a new method for co-phylogenetic tree plotting

Today I have continued to play around with the method I posted yesterday to create a kind of “co-phylogenetic plot” - that is, a plot of left & right facing phylograms with the tips lined up, & connected, so as to show an association between species.

The major improvements that I made are the following:

(1) I improved the tip rotation optimization method, and now allow the user to specify a function for the optimization (such as function(x) x2, which tells cophylo to minimize the sum of squares deviations between the plots; or function(x) abs(x), which tells it to minimize the summed absolute values.

(2) I now permit the trees to have different numbers of tips and thus incomplete matching (some taxa in one or the other trees that have no match in the second).

(3) When no assoc matrix is supplied, cophylo now checks for any taxa with matching labels between the two trees, not just to see if all tip labels match.

(4) Now, one tip in one tree can match to multiple tips in a second (and/or vice versa).

Finally, (5) if no associations are provided (& none can be found), the function simply returns two facing trees to be plotted by plot.cophylo.

In the previous version of this function I was using a slightly modified version of the phytools function minRotate to perform the node rotation optimization. I have replaced this with a custom internal function which is much more flexible and better suited to this particular task.

Here's a demo of some of this functionality:

library(phytools)
source("http://www.phytools.org/cophylo/v0.2/cophylo.R")

First, the basic usage, but specifying different functions to optimize node rotation. The default is x2.

tr1<-pbtree(n=26,tip.label=LETTERS)
tr2<-pbtree(n=26,tip.label=sample(LETTERS))
obj<-cophylo(tr1,tr2,rotate=FALSE)
plot(obj)

obj<-cophylo(tr1,tr2)

## Rotating nodes to optimize matching...
## Done.

plot(obj)

obj<-cophylo(tr1,tr2,fn=function(x) abs(x))

## Rotating nodes to optimize matching...
## Done.

plot(obj)

Now, multiple one tip in tr1 match to multiple tips in tr2 and vice versa:

assoc<-cbind(c("A","A","A","X","Y","Z"),
    c("A","B","C","Z","Z","Z"))
assoc

##      [,1] [,2]
## [1,] "A"  "A" 
## [2,] "A"  "B" 
## [3,] "A"  "C" 
## [4,] "X"  "Z" 
## [5,] "Y"  "Z" 
## [6,] "Z"  "Z"

obj<-cophylo(tr1,tr2,assoc,rotate=FALSE)
plot(obj)

obj<-cophylo(tr1,tr2,assoc)

## Rotating nodes to optimize matching...
## Done.

plot(obj)

Now, a partial matching of tip labels between trees:

tr1<-pbtree(n=12,tip.label=sample(LETTERS[1:12]))
tr2<-pbtree(n=12,tip.label=sample(LETTERS[7:18]))
obj<-cophylo(tr1,tr2)

## Rotating nodes to optimize matching...
## Done.

plot(obj)

Trees with different numbers of tips and partial matching:

tr1<-rtree(n=40)
tr2<-rtree(n=26,tip.label=LETTERS)
assoc<-cbind(sample(tr1$tip.label,20),sample(LETTERS,20))
assoc

##       [,1]  [,2]
##  [1,] "t25" "U" 
##  [2,] "t12" "Z" 
##  [3,] "t37" "A" 
##  [4,] "t22" "N" 
##  [5,] "t39" "H" 
##  [6,] "t9"  "L" 
##  [7,] "t8"  "K" 
##  [8,] "t23" "D" 
##  [9,] "t33" "W" 
## [10,] "t18" "X" 
## [11,] "t1"  "P" 
## [12,] "t4"  "G" 
## [13,] "t5"  "V" 
## [14,] "t19" "T" 
## [15,] "t27" "O" 
## [16,] "t21" "B" 
## [17,] "t6"  "F" 
## [18,] "t13" "S" 
## [19,] "t10" "R" 
## [20,] "t26" "M"

obj<-cophylo(tr1,tr2,assoc)

## Rotating nodes to optimize matching...
## Done.

plot(obj)

Finally, no association provided (& none can be found):

obj<-cophylo(tr1,tr2)

## No associations provided or found.

plot(obj)

## No associations provided.

That's all for now.