2021-12-14R语言批量绘制进化树

setwd('E:\\nwk')
library(ape)
library(ggplot2)
library(ggtree) #加载需要的软件包
group_file <- read.table("samples.group",header = T,row.names = 1)
groupInfo <- split(row.names(group_file), group_file$group)
filename <- list.files(pattern= '.nwk')
func_tree<- function(x){read.tree(x)}
x <- lapply(filename, func_tree)
for (i in 1:length(dir("E:\\nwk/"))){
      name <- filename[i]
      tree <- x[[i]]
      tree <- groupOTU(tree, groupInfo)
      rooted.tree <- root(tree, which(tree$tip.label == "Bol"))
      p<- ggtree(rooted.tree, layout="rectangular", size=0.8,aes(color=group))+ geom_tiplab(size=2)+geom_tippoint(size=1)
      ggsave(p,width = 6, height = 6,file=paste(name,".tiff",sep=""))
 }