A phytools user writes:
“phytools has been a wonderfully helpful package, thanks for this! I have recently been using the
cophylo function and have been finding that specifying the
type parameter has no effect like it
typically does in the
plotSimmap function. I have tried the following:
plot(phytools::cophylo(tree1, tree2, assoc_table, type="cladogram"), ftype="off", type = "cladogram")
cophylo1 <- phytools::cophylo(tree1, tree2, assoc_table, type="cladogram") plot.cophylo(cophylo1, ftype = "off", type="cladogram")
Any help would be greatly appreciated!”
Indeed, this functionality has not existed previously for the
plot.cophylo method in phytools.
It wasn't too hard to include, however, so I just added it.
Here's a quick demo using a co-phylogenetic dataset from Lopez-Vaamonde et al. (2001).
##  '0.7.99'
## load data from Lopez-Vaamonde et al. (2001) data(wasp.trees) data(wasp.data) ## create co-phylogenetic object wasp.cophylo<-cophylo(wasp.trees[],wasp.trees[], assoc=wasp.data)
## Rotating nodes to optimize matching... ## Done.
## plot co-phylogenies plot(wasp.cophylo,link.type="curved",link.lwd=4, link.lty="solid",link.col=make.transparent("red", 0.25),type="cladogram",part=0.45)