丟棄提示後保存節點信息

Question

當我在表中存儲樹和一些節點信息時，我想刪除提示，並相應地修改表。因此，需要在列節點中使用正確的新號碼的新表。

library(ape) 
library(ggtree) 
#make tree 
set.seed(2016-12-31) 
newrtree<-rtree(12) 
newrtreepo<-di2multi(newrtree, tol = 0.5) 

# make table with data to plot in tree 
a<-1:newrtreepo$Nnode # node label 
b<-seq(0,1, length.out=newrtreepo$Nnode) 
c<-1-b 
dat <- data.frame(a=a, b=b,c=c) 
splen<-length(newrtreepo$tip.label) 
dat$node <- splen+1:newrtreepo$Nnode 
dat 
# a   b   c node 
# 1 1 0.0000000 1.0000000 13 
# 2 2 0.1428571 0.8571429 14 
# 3 3 0.2857143 0.7142857 15 
# 4 4 0.4285714 0.5714286 16 
# 5 5 0.5714286 0.4285714 17 
# 6 6 0.7142857 0.2857143 18 
# 7 7 0.8571429 0.1428571 19 
# 8 8 1.0000000 0.0000000 20 

tree5<-ggtree(newrtreepo)+geom_tiplab()+ 
    geom_text2(aes(subset=!isTip, label=node), hjust=-1, check_overlap = T)+ 
    geom_text2(aes(subset=!isTip,x=branch, label=label, size=2), vjust=-.5, hjust=0.5) 

piesa <- nodepie(dat, cols=2:3) 
inset(tree5, piesa) 

droptree2<-drop.tip(newrtreepo,c("t12","t3","t5")) 

Answer 1

我創建的節點標籤爲索引使用修改表。

#modify as in 
newrtreepo$node.label<-paste0("n",1:newrtreepo$Nnode) 
newrtreepo$node.copy<-newrtreepo$node.label 

droptree2<-drop.tip(newrtreepo,c("t12","t3","t5")) 
droptree2$node.label 
# "n1" "n2" "n3" "n5" "n6" "n7" 
droptree2$node.copy 
# "n1" "n2" "n3" "n4" "n5" "n6" "n7" "n8" 

newdatb<-dat[which(droptree2$node.copy %in% droptree2$node.label ==T),] 
rowdat<-nrow(newdatb) 
newlength<-length(droptree2$tip.label) 
newdatb$node <- newlength+1:rowdat 
newdatb 
# a   b   c node 
# 1 1 0.0000000 1.0000000 10 
# 2 2 0.1428571 0.8571429 11 
# 3 3 0.2857143 0.7142857 12 
# 5 5 0.5714286 0.4285714 13 
# 6 6 0.7142857 0.2857143 14 
# 7 7 0.8571429 0.1428571 15 


tree6<-ggtree(droptree2)+geom_tiplab()+ 
    geom_text2(aes(subset=!isTip, label=node), hjust=-1, check_overlap = T)+ 
    geom_text2(aes(subset=!isTip,x=branch, label=label, size=2), vjust=-.5) 

#label as bootstrap 
tree2treedata<-treeio::as.treedata(droptree2, newdatb$a) 
tree7<-ggtree(tree2treedata)+ geom_label(aes(label=bootstrap)) + geom_tiplab()+ 
    geom_text2(aes(subset=!isTip, label=node), hjust=-1, check_overlap = T) 

#create pies of reduced tree 
piesb <- nodepie(newdatb, cols=2:3)#, alpha=.6) 
gridExtra::grid.arrange(inset(tree5, piesa),inset(tree6, piesb),inset(tree7,piesb, width=0.15, height=0.15, 
                     hjust=0.2),ncol=2)