Yesterday a phytools user
the following comment about the function
“Very neat tool to plot barchart next to a tree. Is there a way to color the branches, and also add an axis and axis title to the tree?
Using the following code did nothing to add color the the branch:
for(i in 1:length(tt)) tree<-paintSubTree(tree,node=i,state=tt[i],stem=TRUE) colors<-setNames(c("black","red","blue"),c("KB","PM","KW")) plotTree.barplot(tt,d22, add=TRUE, args.plotTree=list(fsize=1, method="plotSimmap", ftype="reg", colors=colors,lwd=4, use.edge.length = TRUE,axis(1)), args.barplot=list(xlab="Relative abundance",col=phylum_colors, xlim=c(0,1), legend.text=TRUE,args.legend = list(x = "topright", bty="n", xpd = TRUE)))
There is also no free space to plot the legend. Any help is much appreciated.”
Since the commenter hasn't sent me the original data I had to invent some. Here is what they look like:
## ## Phylogenetic tree with 64 tips and 63 internal nodes. ## ## Tip labels: ## t10, t60, t61, t45, t20, t52, ... ## ## Rooted; includes branch lengths.
## t10 t60 t61 t45 t20 t52 ## 0.90532233 0.28482390 0.58228935 0.67411616 0.91762887 0.72831160 ## t53 t48 t17 t43 t44 t22 ## 0.90828956 0.73272700 0.96101692 0.14584122 0.05139047 0.28754064 ## t50 t51 t2 t56 t57 t21 ## 0.65900185 0.10136811 0.92964094 0.56752999 0.14451551 0.26363247 ## t41 t42 t11 t37 t38 t58 ## 0.97087520 0.86466752 0.07710963 0.25440640 0.49022645 0.38157265 ## t59 t36 t25 t7 t26 t27 ## 0.87092899 0.05497484 0.15975640 0.51522823 0.55614193 0.94013214 ## t3 t32 t33 t39 t40 t34 ## 0.42338521 0.40184781 0.38844121 0.47471898 0.63702061 0.13603071 ## t35 t4 t63 t64 t62 t15 ## 0.13721665 0.47143131 0.11097818 0.44565765 0.84875954 0.83262279 ## t16 t28 t29 t6 t46 t47 ## 0.57204090 0.24215227 0.89643177 0.31423521 0.27973032 0.57452690 ## t12 t13 t1 t8 t9 t24 ## 0.78650892 0.18264281 0.53596682 0.37515409 0.66952881 0.02464721 ## t54 t55 t49 t30 t31 t23 ## 0.95914836 0.61207190 0.71294626 0.75437136 0.78962420 0.96600007 ## t14 t18 t19 t5 ## 0.89622112 0.64615452 0.07087410 0.54074719
Now, this inquiry had many parts. If I have them right, he or she wants to:
1) Add a axis & axis title to the tree. 2) Leave space on the barplot for a legend & add it. 3) Color the edges of the tree by painting subtrees different colors.
All of this is possible - though not necessarily in the way the commenter imagines.
In addition, I had to push a couple of small updates to
get the following to work exactly as hoped. These can be obtained simply by updating
phytools from GitHub. If you don't want to do that this second you can instead load
the function from source as follows (although I recommend updating phytools the
next time you restart R):
Now we're ready! Let's see it:
## first paint sub trees tree<-paintSubTree(tree,81,"PM","KB") tree<-paintSubTree(tree,107,"KW","KB") ## set colors colors<-setNames(c("black","red","blue"),c("KB","PM","KW"))
Next I'm going to pull the 'states' (based on my above painting) from the tips. This is just to color the bars using the same scheme as I've used for the edges of the tree.
ss<-getStates(tree,"tips") barcols<-setNames(sapply(ss,function(x,y) y[which(names(y)==x)], y=colors),names(ss))
Now I'm ready to plot. Note that my initial plot is of a plain tree to the level panel - but then I will replot the tree in that space using the same parameters.
plotTree.barplot(tree,x[tree$tip.label],args.plotTree=list(ftype="off"), args.barplot=list(col=barcols,border=barcols,xlab="", xlim=c(0,1.3)),args.axis=list(at=seq(0,1,by=0.2))) legend(x="topright",legend=names(colors),pch=22,pt.cex=2,pt.bg=colors, box.col="transparent") mtext("relative abundance",1,at=0.5,line=2.5) ## this is how I go back to my tree frame par(mfg=c(1,1)) plot(tree,colors,ftype='off',mar=c(5.1,1.1,2.1,0)) axis(1,at=seq(0,50,by=50)) mtext("time",1,at=25,line=2)
Neat. That's basically what I wanted.
FYI, the following shows how the tree & data were simulated for this demo:
set.seed(10) tree<-pbtree(n=64,scale=100) x<-fastBM(tree,sig2=0.1,bounds=c(0,1))
I would like to change the tip.labels colours on a phylogeny based on a discrete trait value in a traits data.frame.
What is a method to do this? The above is a step too far for me at this stage.
Thanks a lot,
Thank you for providing cool examples for what we can do with this package! I have a non-ultrametric tree and I would like to plot next to a bar chart. I can't seem to both align tip labels (with dotted lines) and get the barplot to show. Is there a method for this?ReplyDelete