Add legend into ggtree (ggplot) R

Question

I'm building a tree with ggtree on R.

library(ggtree)

here is the newick file content:

tree = read.newick("newick_tree")

Here is the code I use:

colfunc <- colorRampPalette(c("red", "blue"))
col=colfunc(110)


for (i in 1:length(tree$node.label)){
  if(as.vector(tree$node.label[i])>0.99){
    col[i]<-'#CB1414'
  } else if(as.vector(tree$node.label[i])>0.90 & (as.vector(tree$node.label[i]) < 0.99)){
    col[i]<-'#F0F014'
  } else if(as.vector(tree$node.label[i])>0.76 & (as.vector(tree$node.label[i]) < 0.90)){
    col[i]<-'#098527'
  } else if(as.vector(tree$node.label[i])>0.51 & (as.vector(tree$node.label[i]) < 0.76)){
    col[i]<-'#18D8F7'
  } else if(as.vector(tree$node.label[i])>0 & (as.vector(tree$node.label[i]) < 0.50)){
    col[i]<-'#1B72DB'
  }
}
p<-ggtree(tree,size=0.5,branch.length="none")   +geom_tiplab(size = 2, col ="black")  + geom_nodepoint(color=col, alpha=1, size=1.5, show.legend = TRUE)+ 
  geom_treescale(x=30, y=1)

In order to get point color depending on the bootstrap level I used this part: geom_nodepoint(color=col, alpha=1, size=1.5, show.legend = TRUE) where col is a variable such as:

> col
  [1] "#CB1414" "#FC0002" "#FA0004" "#F70007" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414"
 [15] "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#F0F014" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414"
 [29] "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414"
 [43] "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#F0F014" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#098527" "#CB1414"
 [57] "#CB1414" "#18D8F7" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414"
 [71] "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#F0F014" "#098527" "#098527" "#CB1414"
 [85] "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#F0F014" "#CB1414" "#098527" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#1B72DB"
 [99] "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414" "#CB1414"

That I made depending on the number in this variable:

> tree$node.labe
  [1] "1"    ""     ""     "0.99" "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"   
 [21] "1"    "0.97" "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"   
 [41] "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "0.98" "1"    "1"    "1"    "1"    "0.89" "1"    "1"    "0.64" "1"    "1"   
 [61] "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"   
 [81] "0.92" "0.8"  "0.77" "1"    "1"    "1"    "1"    "1"    "0.96" "1"    "0.84" "1"    "1"    "1"    "1"    "1"    "1"    "0.48" "1"    "1"   
[101] "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"    "1"

And now I just would like to display the 5 ranges color legend in the tree such as :

but the option show.legend = TRUE does not work for that. Does anyone have an idea? I also tried to add p + theme(legend.position="right") but there is still no legend.

Thank you for your help.

here is the deput(tree)

@MarcoSandri sure, the code is in the comment below – chippycentra Apr 17 '19 at 12:54 — chippycentra, Apr 17 '19 at 12:54

score 2 · Accepted Answer · answered Apr 17 '19 at 22:02

The number of node points in your tree is 221, with 111 final points. Thus, your col vector needs to have 221 elements; the first 111 specify the colors of the final points.
Here is a way to create the proper col vector starting from tree$node.label:

x <- c(rep(NA,111), as.numeric(tree$node.label)*100)
col <- cut(x, breaks=c(0,50,75,90,99,100))
col <- factor(col, levels=rev(levels(col)))
col <- factor(col, labels=c("100%","91-99%","76-90%","51-75%","0-50%"))

Node points can be colored using the color aesthetic:

library(ggtree)
library(ggplot2)
p <- ggtree(tree, size=0.5,branch.length="none")   +
    geom_tiplab(size = 2, col ="black")  + 
    geom_point(aes(color=col), alpha=1, size=1.5, show.legend = TRUE) + 
    geom_treescale(x=30, y=1) +
    theme(legend.position="right") +
    scale_colour_manual(na.translate = F, name="Bootstrap support",
                        values=c("#CB1414","#F0F014","#098527","#18D8F7","#1B72DB")) +
    guides(color = guide_legend(override.aes = list(size = 5))) 
p

Thank you very much it was exactly what I needed! – chippycentra Apr 18 '19 at 08:12 — chippycentra, Apr 18 '19 at 08:12

Add legend into ggtree (ggplot) R

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