使用R语言的phytools包在进化树上标记自己测序取样的样本

library(ggtree)
library(phytools)
tree <- read.tree("data/20220829/fig2.nwk")
plotTree(tree)

lapply(c("A","H","J"),grep,tree$tip.label) -> tips

lapply(tips,phangorn::Ancestors,x=tree,type="all") %>% 
  unlist() %>% unique() -> parents

c(tips %>% unlist(),parents) -> nodes

## 可以把根节点去掉
setdiff(nodes,Ntip(tree)+1) -> nodes

paintBranches(tree,
              nodes,
              state = "1",
              anc.state = "0") -> tree03

cols<-setNames(c("gray","black"),0:1)
plot(tree03,
     lend=1,
     add=TRUE,
     split.vertical=TRUE,
     color=cols)