Yesterday I received the following inquiry about phytools:
“I am using your package to create stochastic character maps in R and I have not had any luck offsetting the species names when creating my fan trees. Do you have any suggestions about how this can be fixed, it would be greatly appreciated.”
In fact, label offset is not an option in
plot.simmap(...,type="fan"); however the following is a fairly
elegant hack I thought of this morning:
library(phytools) library(geiger) data(anoletree) ## our tree that we will use for this example anoletree
## ## Phylogenetic tree with 82 tips and 81 internal nodes. ## ## Tip labels: ## Anolis_ahli, Anolis_allogus, Anolis_rubribarbus, Anolis_imias, Anolis_sagrei, Anolis_bremeri, ... ## ## The tree includes a mapped, 6-state discrete character with states: ## CG, GB, TC, TG, Tr, Tw ## ## Rooted; includes branch lengths.
## first plot the tree with transparent color: h<-max(nodeHeights(anoletree)) offset.factor<-1.05 ## increase this for greater offset plotTree(rescale(anoletree,model="depth",depth=offset.factor*h), color="transparent",ftype="i",type="fan",fsize=0.7,lwd=3) par(fg="transparent") obj<-get("last_plot.phylo",envir=.PlotPhyloEnv) plot(anoletree,type="fan",fsize=0.7,ftype="i",add=TRUE, xlim=obj$x.lim,ylim=obj$y.lim,lwd=3)
## no colors provided. using the following legend: ## CG GB TC TG Tr Tw ## "black" "red" "green3" "blue" "cyan" "magenta"
par(fg="black") ## add a legend states<-sort(unique(getStates(anoletree,"tips"))) add.simmap.legend(x=obj$x.lim,y=obj$y.lim, colors=setNames(palette()[1:length(states)],states), prompt=FALSE)
That's the hack.
Liam, this hack is awesome, really makes the plot more clear. For some reason when I add in the simmap legend, I'm only getting squares with the correct colors, but no text. When I plot the tree and the legend normally it works just fine. Any thoughts on what might be happening? Thanks.ReplyDelete
Yes. You probably didn't set:Delete
before adding the legend. - Liam
This blog totally steps away from all those generic and symbolizes what well-written truly looks like.ReplyDelete
Hi Liam, how to do the same for contMap object?ReplyDelete
Hi Liam, I'm totally new to phytools and it's great. I have the same question as the person above, can this method be adapted to work with conMap? Thank youReplyDelete