Tuesday, May 2, 2017

Incorporating raster images into a plotted tree

Here is a demo of some code to add raster images (e.g., .jpg, .png) to a plotted tree in R.

In this case, the images are .png files with a transparent background (which makes things nice, but they needed be. I pulled the images from a reptile dealer website where they are presented without attribution.

This specific example uses the development version of phytools which can be installed from GitHub using devtools.

library(phytools)
library(png)
anole.tree<-read.tree("Anolis.tre")
anole.tree
## 
## Phylogenetic tree with 100 tips and 99 internal nodes.
## 
## Tip labels:
##  ahli, allogus, rubribarbus, imias, sagrei, bremeri, ...
## 
## Rooted; includes branch lengths.
svl<-as.matrix(read.csv("svl.csv",header=TRUE,row.names=1))[,1]
svl
##            ahli         alayoni         alfaroi        aliniger 
##        4.039125        3.815705        3.526655        4.036557 
##        allisoni         allogus   altitudinalis         alumina 
##        4.375390        4.040138        3.842994        3.588941 
##       alutaceus     angusticeps     argenteolus     argillaceus 
##        3.554891        3.788595        3.971307        3.757869 
##         armouri   bahorucoensis        baleatus        baracoae 
##        4.121684        3.827445        5.053056        5.042780 
##       barahonae        barbatus        barbouri        bartschi 
##        5.076958        5.003946        3.663932        4.280547 
##         bremeri        breslini    brevirostris        caudalis 
##        4.113371        4.051111        3.874155        3.911743 
##       centralis  chamaeleonides    chlorocyanus     christophei 
##        3.697941        5.042349        4.275448        3.884652 
##       clivicola     coelestinus        confusus           cooki 
##        3.758726        4.297965        3.938442        4.091535 
##    cristatellus    cupeyalensis         cuvieri    cyanopleurus 
##        4.189820        3.462014        4.875012        3.630161 
##         cybotes     darlingtoni       distichus dolichocephalus 
##        4.210982        4.302036        3.928796        3.908550 
##       equestris      etheridgei   eugenegrahami       evermanni 
##        5.113994        3.657991        4.128504        4.165605 
##         fowleri         garmani         grahami           guafe 
##        4.288780        4.769473        4.154274        3.877457 
##       guamuhaya         guazuma       gundlachi       haetianus 
##        5.036953        3.763884        4.188105        4.316542 
##      hendersoni      homolechis           imias    inexpectatus 
##        3.859835        4.032806        4.099687        3.537439 
##       insolitus        isolepis           jubar           krugi 
##        3.800471        3.657088        3.952605        3.886500 
##      lineatopus   longitibialis        loysiana          lucius 
##        4.128612        4.242103        3.701240        4.198915 
##    luteogularis      macilentus        marcanoi          marron 
##        5.101085        3.715765        4.079485        3.831810 
##         mestrei       monticola          noblei        occultus 
##        3.987147        3.770613        5.083473        3.663049 
##         olssoni        opalinus      ophiolepis        oporinus 
##        3.793899        3.838376        3.637962        3.845670 
##        paternus        placidus       poncensis        porcatus 
##        3.802961        3.773967        3.820378        4.258991 
##          porcus      pulchellus         pumilis quadriocellifer 
##        5.038034        3.799022        3.466860        3.901619 
##      reconditus        ricordii     rubribarbus          sagrei 
##        4.482607        5.013963        4.078469        4.067162 
##    semilineatus        sheplani         shrevei      singularis 
##        3.696631        3.682924        3.983003        4.057997 
##      smallwoodi         strahmi       stratulus     valencienni 
##        5.035096        4.274271        3.869881        4.321524 
##       vanidicus    vermiculatus        websteri       whitemani 
##        3.626206        4.802849        3.916546        4.097479
obj<-contMap(anole.tree,svl,plot=FALSE)
obj
## Object of class "contMap" containing:
## 
## (1) A phylogenetic tree with 100 tips and 99 internal nodes.
## 
## (2) A mapped continuous trait on the range (3.462014, 5.113994).
obj<-setMap(obj,invert=TRUE)
plot(obj,type="fan",outline=FALSE,fsize=c(0.6,1),legend=1,
    lwd=c(4,8),xlim=c(-1.8,1.8),leg.txt="log(SVL)")
spp<-c("barbatus","porcatus","cristatellus","equestris","sagrei")
w<-0.5
for(i in 1:length(spp)){
    xy<-add.arrow(obj,spp[i],col="transparent",arrl=0.45,lwd=3,hedl=0.1)
    arrl<-if(spp[i]%in%c("sagrei","porcatus")) 0.24 
        else if(spp[i]=="barbatus") 0.2 else 0.34
    add.arrow(obj,spp[i],col="blue",arrl=arrl,lwd=3,hedl=0.05)
    img<-readPNG(source=paste(spp[i],".png",sep=""))
    asp<-dim(img)[1]/dim(img)[2]
    rasterImage(img,xy$x0-w/2,xy$y0-w/2*asp,xy$x0+w/2,xy$y0+w/2*asp)
}

plot of chunk unnamed-chunk-1

We can also make output this as a PDF as follows and the result is quite nice:

pdf(file="anole.contMap-imgs.pdf",width=10,height=10)
plot(obj,type="fan",outline=FALSE,fsize=c(0.8,1),legend=1,
    lwd=c(4,8),xlim=c(-1.8,1.8),leg.txt="log(SVL)")
spp<-c("barbatus","porcatus","cristatellus","equestris","sagrei")
library(png)
w<-0.5
for(i in 1:length(spp)){
    xy<-add.arrow(obj,spp[i],col="transparent",arrl=0.45,lwd=3,hedl=0.1)
    arrl<-if(spp[i]%in%c("sagrei","porcatus")) 0.24 
        else if(spp[i]=="barbatus") 0.2 else 0.34
    add.arrow(obj,spp[i],col="blue",arrl=arrl,lwd=3,hedl=0.05)
    img<-readPNG(source=paste(spp[i],".png",sep=""))
    asp<-dim(img)[1]/dim(img)[2]
    rasterImage(img,xy$x0-w/2,xy$y0-w/2*asp,xy$x0+w/2,xy$y0+w/2*asp)
}
dev.off()
## png 
##   2

That's all.

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