Nothing
knitr::opts_chunk$set(echo = TRUE) suppressMessages(library(magrittr))
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") } phycanv
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