Question: How do I show bootstrap values in the phylogenetic tree using R?
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gravatar for lhernanj
6 months ago by
lhernanj0
lhernanj0 wrote:

Hello guys, I am having a difficult time figuring out how to show the bootstrap values in my tree. I am looking for an easy answer because I am not expert in R. I just done a RaxML tree and exported my results to R. I got constructed a fine figure, but I don't know how to show bootstrap values in that. Please look at my R code:

setwd("/home/SUMMARY_2018/TREES") 
raxml.tree <- read.tree(file.path("RAxML_bipartitionsBranchLabels.job3"))
raxml.bootstrap <- read.tree(file.path("RaxML_bootstrap.job2"))

raxml<- rep("black", length(raxml.tree$tip.label))
categorias<- c("A5190.1","Z21068.1")
colorcategorias<-c("red","red")

for(i in 1:length(categorias)){
  raxml[grep(categorias[i], raxml.tree$tip.label)] <- colorcategorias[i]
}
edgecol<- rep("black", nrow(raxml.tree$edge))
edgecol[23:61]<- "blue" 
edgecol[73:75]<- "blue"

plot(unroot(raxml.tree),title("A", line=-2, adj=0.3), use.edge.length =TRUE, tip.color= raxml, type="unrooted", show.tip.label = TRUE, cex= 0.7, no.margin= TRUE, lab4ut = "axial", edge.width = 2, edge.color = edgecol, show.node.label=TRUE)

as you can see I open my bootstrap file but I am not sure about how should I manipulate it.

I would thank some of help.

phytools phylogenetic tree R • 369 views
ADD COMMENTlink modified 8 weeks ago • written 6 months ago by lhernanj0
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