Is it possible to highlight clade by tip labels in ggtree (A_ and B_ in the example below)? Finding node numbers is really annoying especially when you have more than 1000 tips.
set.seed(2015-12-21)
tree <- rtree(30)
tree$tip.label <- c(paste0(rep("A_", 15), rep(1:15)), paste0(rep("B_", 14), rep(1:14)), "C_1")
ggtree(tree) + geom_highlight(node = 33) + geom_tiplab() + xlim(NA, 8)
specify id's first
id <- c("A_", "B_", "C_")
then use the ape package to find MRCA nodes
parent_nodes <- sapply(id, function(x) ape::getMRCA(tree, tree$tip.label[str_detect(tree$tip.label, x)]))
parent_nodes
$A_
[1] 33
$B_
[1] 47
$C_
NULL
and use them to highligth clades:
g <- ggtree(tree)
g + geom_j
The technical post webpages of this site follow the CC BY-SA 4.0 protocol. If you need to reprint, please indicate the site URL or the original address.Any question please contact:yoyou2525@163.com.