Markdown test

A ggtree Script

this is the document to modify a tree

---

library(ggtree)  
library("tidyr")  
library(dplyr)  
library("ggplot2")  
library(ggstance)  
library(ggsci)  
library(extrafont)  
library("yyplot")  

tree1<-read.newick("rooted.nwk",node.label = "support")  
tmp<-tree1@data[-1,]  
data1<-read.table("countresult.txt",header = F,sep = "\t")  
colnames(data1)<-c("support","type","num")  
dat1<-spread(data1,key = "type",value = "num")  
dat2<-dat1[1:39,]  
dat1<-dat1[40:74,]  
cols=pal_aaas()(4)  
dat1$support<-gsub("X","",dat1$support)  
tmp$support<-as.character(tmp$support)  
dat1<-left_join(x = dat1,y=tmp,by="support")  
dat2<-dat1[,-c(1,2,6)]  

Begin to Plot

---

p<-ggtree(tree1)  
p$data$x[1]<-0.05  
p$data$x[2]<-0.05  
p<-p+geom_tiplab(align = T)+theme_tree2()+xlim(c(0,0.2))  
dat2<--dat2  
dat2$node<-(-dat2$node)  

bars<-nodebar(dat2,cols=1:4,position = "dodge",color = c(gain='red',expansion='orange',loss="black",reduction='grey'))  

for (i in names(bars))  
  {  
bars[[i]]<-bars[[i]]+coord_flip()  
  }  
p1<-inset(p, bars, width=.01, height=2,hjust=.003)  
pt<-p1 %<+% dat1+geom_nodelab(aes(label=current),nudge_x = 0.003,size=3)  

╮(￣▽￣)╭

Da Huo
[email protected]
Institute of hydrobiology,Chinese Academy of Science