Nothing
## ----setup, include=FALSE------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
suppressMessages(library(magrittr))
## ----warning=FALSE-------------------------------------------------------
library(magrittr)
library(ape)
library(phylocanvas)
data("bird.families")
phylocanvas(bird.families, treetype = "radial",
width = 700, textsize = 10, nodesize = 10)
## ----warning=FALSE-------------------------------------------------------
# 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)
## ---- warning=FALSE------------------------------------------------------
phylocanvas(birds, width = 700, textsize = 10, nodesize = 10, treetype = "radial") %>%
select_branch(nodeid=nodename, cascade=T)
## ----warning=FALSE-------------------------------------------------------
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
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.