library(ape)
library(phylobase)
library(phylocanvas)
birdfile <- system.file("treedata/birdfamilies.tree", package="phylocanvas")
birdfamilies <- load.tree(birdfile)
tree <- load.tree(birdfile)
tree <- birdfamilies
phy1 <- phylocanvas(tree)
phy1
Highlight the most recent common ancestor (MRCA).
# get MRCA
n1 <- MRCA(tree, c("Cerylidae", "Upupidae"))
n1 <- names(n1)
# highlight all submembers of the MRCA
phylocanvas(tree, width = 700) %>% select_branch(nodeid=n1, cascade=T)
phylocanvas(tree, width = 700, treetype = "radial") %>%
select_branch(nodeid=n1, cascade=T)
To highlight multiple clades, you can identify clades by node number, in this case by MRCA. Then you can stylize the descendant nodes.
phycanv <- phylocanvas(tree, width = 700, treetype = "radial")
nodenames <- get.descendants(tree, n1)
clade2names <- get.descendants(tree, names(MRCA(tree, c("Pteroclidae", "Jacanidae"))))
clade3names <- get.descendants(tree, names(MRCA(tree, c("Irenidae", "Paramythiidae"))))
for (nodename in nodenames) {
phycanv <- style_node(phycanv, nodeid = nodename, fillcolor="green")
}
for (nodename in clade2names) {
phycanv <- style_node(phycanv, nodeid = nodename, fillcolor="red")
}
for (nodename in clade3names) {
phycanv <- style_node(phycanv, nodeid = nodename, fillcolor="blue")
}
phycanv