Following a suggestion by Eliot
Miller, I have added some additional user control to the S3
plot method for objects of class "cophylo". These
options now permit user control of basically all aspects of the linking
lines - from the line type (argument link.lty), to the line
color (link.col) and line width (link.lwd). These
arguments can be supplied as a single value, or as a vector with a length
equal to the number of rows in the association table, assoc.
These updates can be seen
here.
I also added a summary method for the object class that prints
out the association table, assoc, along with some other
information about the object. This update I pushed separately and can be viewed
here.
We can try it out as follows:
library(phytools)
t1
##
## Phylogenetic tree with 20 tips and 19 internal nodes.
##
## Tip labels:
## Z._szgp, D._hgpq, K._ogeszq, D._xhwpobav, S._oyqfmig, Q._bchviyf, ...
##
## Rooted; includes branch lengths.
t2
##
## Phylogenetic tree with 40 tips and 39 internal nodes.
##
## Tip labels:
## G._tbvmo, I._hrtmxoy, D._qonmgjx, E._dlmov, X._pinwva, C._zpekl, ...
##
## Rooted; includes branch lengths.
assoc
## [,1] [,2]
## D "D._hgpq" "Q._eocwr"
## D "D._hgpq" "B._galucwd"
## D "D._hgpq" "E._helanvgx"
## D "D._xhwpobav" "E._dlmov"
## D "D._xhwpobav" "C._zpekl"
## E "E._chlauw" "S._stcn"
## E "E._chlauw" "Q._eocwr"
## E "E._poqyd" "D._jlrpfati"
## E "E._poqyd" "C._zpekl"
## E "E._poqyd" "Q._eocwr"
## E "E._poqyd" "I._zjyhw"
## F "F._djztolsb" "K._tiwfhler"
## F "F._djztolsb" "E._dlmov"
## I "I._infumtpg" "G._tbvmo"
## I "I._ymzacesf" "D._qonmgjx"
## I "I._ymzacesf" "C._zpekl"
## K "K._guxhip" "W._xgapntmd"
## K "K._guxhip" "B._qtkl"
## K "K._hswluo" "B._galucwd"
## K "K._ogeszq" "C._zpekl"
## L "L._pgayvzc" "Q._eocwr"
## L "L._pgayvzc" "K._tiwfhler"
## M "M._vksyp" "G._tbvmo"
## M "M._vksyp" "D._pqfdcnsx"
## M "M._vksyp" "S._stcn"
## N "N._panljtox" "W._xgapntmd"
## N "N._panljtox" "O._ytjn"
## Q "Q._bchviyf" "D._pqfdcnsx"
## Q "Q._bchviyf" "S._stcn"
## Q "Q._bchviyf" "A._ahodzte"
## Q "Q._iqzp" "O._ytjn"
## S "S._oyqfmig" "B._qtkl"
## S "S._oyqfmig" "A._ahodzte"
## S "S._oyqfmig" "E._helanvgx"
## Y "Y._itpzkvc" "I._zjyhw"
## Y "Y._itpzkvc" "D._qonmgjx"
## Y "Y._vnlf" "D._jlrpfati"
## Z "Z._szgp" "S._stcn"
## Z "Z._szgp" "B._fvakurtm"
## Z "Z._szgp" "B._fvakurtm"
obj<-cophylo(t1,t2,assoc)
## Rotating nodes to optimize matching...
## Done.
summary(obj)
##
## Co-phylogenetic ("cophylo") object: obj
##
## Tree 1 (left tree) is an object of class "phylo" containing 20 species.
##
## Tree 2 (right tree) is an object of class "phylo" containing 40 species.
##
## Association (assoc) table as follows:
##
## left: ---- right:
## D._hgpq ---- Q._eocwr
## D._hgpq ---- B._galucwd
## D._hgpq ---- E._helanvgx
## D._xhwpobav ---- E._dlmov
## D._xhwpobav ---- C._zpekl
## E._chlauw ---- S._stcn
## E._chlauw ---- Q._eocwr
## E._poqyd ---- D._jlrpfati
## E._poqyd ---- C._zpekl
## E._poqyd ---- Q._eocwr
## E._poqyd ---- I._zjyhw
## F._djztolsb ---- K._tiwfhler
## F._djztolsb ---- E._dlmov
## I._infumtpg ---- G._tbvmo
## I._ymzacesf ---- D._qonmgjx
## I._ymzacesf ---- C._zpekl
## K._guxhip ---- W._xgapntmd
## K._guxhip ---- B._qtkl
## K._hswluo ---- B._galucwd
## K._ogeszq ---- C._zpekl
## L._pgayvzc ---- Q._eocwr
## L._pgayvzc ---- K._tiwfhler
## M._vksyp ---- G._tbvmo
## M._vksyp ---- D._pqfdcnsx
## M._vksyp ---- S._stcn
## N._panljtox ---- W._xgapntmd
## N._panljtox ---- O._ytjn
## Q._bchviyf ---- D._pqfdcnsx
## Q._bchviyf ---- S._stcn
## Q._bchviyf ---- A._ahodzte
## Q._iqzp ---- O._ytjn
## S._oyqfmig ---- B._qtkl
## S._oyqfmig ---- A._ahodzte
## S._oyqfmig ---- E._helanvgx
## Y._itpzkvc ---- I._zjyhw
## Y._itpzkvc ---- D._qonmgjx
## Y._vnlf ---- D._jlrpfati
## Z._szgp ---- S._stcn
## Z._szgp ---- B._fvakurtm
## Z._szgp ---- B._fvakurtm
plot(obj,fsize=c(1,0.8)) ## basic method
Now, let's change the linking line width by some criterion - say, the number of links from each tip for the tree on the left:
lwd<-summary(as.factor(obj$assoc[,1]))
lwd
## D._hgpq D._xhwpobav E._chlauw E._poqyd F._djztolsb I._infumtpg
## 3 2 2 4 2 1
## I._ymzacesf K._guxhip K._hswluo K._ogeszq L._pgayvzc M._vksyp
## 2 2 1 1 2 3
## N._panljtox Q._bchviyf Q._iqzp S._oyqfmig Y._itpzkvc Y._vnlf
## 2 3 1 3 2 1
## Z._szgp
## 3
lwd<-lwd[obj$assoc[,1]]
lwd
## D._hgpq D._hgpq D._hgpq D._xhwpobav D._xhwpobav E._chlauw
## 3 3 3 2 2 2
## E._chlauw E._poqyd E._poqyd E._poqyd E._poqyd F._djztolsb
## 2 4 4 4 4 2
## F._djztolsb I._infumtpg I._ymzacesf I._ymzacesf K._guxhip K._guxhip
## 2 1 2 2 2 2
## K._hswluo K._ogeszq L._pgayvzc L._pgayvzc M._vksyp M._vksyp
## 1 1 2 2 3 3
## M._vksyp N._panljtox N._panljtox Q._bchviyf Q._bchviyf Q._bchviyf
## 3 2 2 3 3 3
## Q._iqzp S._oyqfmig S._oyqfmig S._oyqfmig Y._itpzkvc Y._itpzkvc
## 1 3 3 3 2 2
## Y._vnlf Z._szgp Z._szgp Z._szgp
## 1 3 3 3
plot(obj,fsize=c(1,0.8),link.lwd=lwd,link.lty="solid")
We can do the line colors by the same criterion:
col<-heat.colors(n=max(lwd))[max(lwd)-lwd+1]
plot(obj,fsize=c(1,0.8),link.lwd=lwd,
link.lty="solid",link.col=col)
Or, using link.type="curved", here I'll also make the
linking lines semi-transparent:
par(lend=1) ## change to square lend
plot(obj,fsize=c(1,0.8),link.lwd=lwd,link.lty="solid",
link.col=sapply(col,make.transparent,0.6),
link.type="curved")
(although it gets a little messy for these random data).
This example was simulated as follows:
library(phytools)
t1<-rtree(n=20,tip.label=
sapply(sample(LETTERS,20,replace=TRUE),
function(x)
paste(x,paste(sample(letters,sample(4:8,1)),
collapse=""),sep="._")))
t2<-rtree(n=40,tip.label=
sapply(sample(LETTERS,40,replace=TRUE),
function(x)
paste(x,paste(sample(letters,sample(4:8,1)),
collapse=""),sep="._")))
assoc<-cbind(sample(t1$tip.label,40,replace=TRUE),
sample(t2$tip.label,20,replace=TRUE))
ii<-order(assoc[,1])
assoc<-assoc[ii,]
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