Wednesday, September 18, 2013

Coloring tip labels by character state

Yesterday I received the query:

"I want to color my tree tip labels according to a particular character and provide a legend for the same."

Here's a demo of one way to do this, using the phytools data object anoletree:

require(phytools)
data(anoletree)
tree<-anoletree
x<-getStates(tree,"tips")
par(fg="transparent")
plotTree(tree,fsize=0.6,ylim=c(-1,length(tree$tip.label)))
lastPP<-get("last_plot.phylo",env=.PlotPhyloEnv)
ss<-sort(unique(x))
colors<-setNames(palette()[1:length(ss)],ss)
par(fg="black")
add.simmap.legend(colors=colors,vertical=FALSE,x=0.25,
  y=-1,prompt=FALSE)
colors<-sapply(x,function(x,y) y[which(names(y)==x)],
  y=colors)
tt<-gsub("_"," ",tree$tip.label)
text(lastPP$xx[1:length(tt)],lastPP$yy[1:length(tt)],
  tt,cex=0.6,col=colors,pos=4,offset=0.1,font=3)

Here's the result:

Obviously, some of this is idiosyncratic to this specific dataset. Hopefully, users can figure out how to modify this to their own data and problem.

5 comments:

  1. Thanks for this code! I have binary states and can't quite seem to tweak the code right. I can assign the colors (black or red) based on the binary state, but when I try to write the text to the figure the colors come out jumbled. Thoughts?

    ReplyDelete
  2. If you have a vector colors with the colors you want for the tips, and names(colors) equal to the tip names sort by the vector tip.label & try:

    colors<-colors[tree$tip.label]

    Let us know if that does the trick. Liam

    ReplyDelete
  3. I have a question for you. The part of the code

    lastPP<-get("last_plot.phylo",env=.PlotPhyloEnv)
    tt<-gsub("_"," ",tree$tip.label)
    text(lastPP$xx[1:length(tt)],lastPP$yy[1:length(tt)],
    tt,cex=0.6,col=colors,pos=4,offset=0.1,font=3)

    can help me to extract the x and y coordinates where the tips are located?
    I want to plot some boxplots on the tips of the tree but the location of them has proven to be difficult, so I was wondering if this will help me align the boxplots to the tips.

    ReplyDelete
  4. Hi Liam,
    Do you have a suggestion for changing the tip colors to correspond to a discrete character (as in the example above) in the function phenogram, while preserving the spread.labels?
    Thanks!

    ReplyDelete
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