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library(magrittr)
library(ape)
library(phylocanvas)
data("bird.families")
phylocanvas(bird.families, treetype = "radial",
width = 700, textsize = 10, nodesize = 10)Highlight the most recent common ancestor (MRCA).
# add internal nodenames
birds <- makeNodeLabel(bird.families)
# convert to phylo4 which has a few nice convenicnece methods including the
# ability to get names with nodes.
birds <- phylobase::phylo4(birds)
# get MRCA
node <- phylobase::MRCA(birds,c("Cerylidae", "Upupidae"))
# get the node name
nodename <- names(node)
# highlight all submembers of the MRCA
phylocanvas(birds, width = 700, textsize = 10, nodesize = 10) %>%
select_branch(nodeid=nodename, cascade=T)phylocanvas(birds, width = 700, textsize = 10, nodesize = 10, treetype = "radial") %>%
select_branch(nodeid=nodename, cascade=T)To highlight multiple clades, you can identify clades by node nubmer, in this case by MRCA. Then you can stylize the descendant nodes.
phycanv <- phylocanvas(birds, width = 700, textsize = 10, nodesize = 10, treetype = "radial")
nodenames <- get.descendants(birds, nodename)
clade2names <- get.descendants(birds, phylobase::MRCA(birds, c("Pteroclidae", "Jacanidae")))
for (nodename in nodenames) {
phycanv <- style_node(phycanv, nodeid = nodename, fillcolor="green")
}
for (nodename in clade2names) {
phycanv <- style_node(phycanv, nodeid = nodename, fillcolor="red")
}
phycanvThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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