Entering edit mode
6.2 years ago
lhernanj
•
0
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.