Friday, June 7, 2019

The phylogenetic multivariate scattergram for continuous traits

I just pushed another couple of new updates to phytools (1, 2).

First, I added two new functions to the namespace, phenogram95 and phyloScattergram. These previously existed in the package but as options within the plotting function fancyTree. The phenogram95 method is quite popular, but the 'phylogenetic scattergram' I'd yet to see used in publication. I have also added some additionally flexibility to the latter function which perhaps might help it see some more use.

Second, I created a new S3 method called setMap. On "densityMap" and "contMap" objects this should work exactly the same as the old setMap function, but it will also work for the "phyloScattergram" object without having to call a differently named function.

Here's a demo of the 'new' phyloScattergram function & setMap S3 method.

First, with some simulated data:

library(phytools)
tree<-pbtree(n=26,tip.label=LETTERS)
V<-matrix(c(
    1.0,0.7,0.0,
    0.7,1.4,0.0,
    0.0,0.0,0.5),3,3)
X<-sim.corrs(tree,V)
object<-phyloScattergram(tree,X,fixed.lims=TRUE)
## Computing multidimensional phylogenetic scatterplot matrix...

plot of chunk unnamed-chunk-1

object
## 
## Object of class "phyloScattergram" for 3 continuous traits.
## To replot enter "plot(object_name)" at the prompt.
object<-setMap(object,c("yellow","black"))
plot(object,ftype="off")

plot of chunk unnamed-chunk-1

Next, here are some real data that I pulled off of Dryad:

liolaemus<-read.tree(file=
    "https://datadryad.org/bitstream/handle/10255/dryad.169645/liolaeminipl.phy")
liolaemus<-drop.tip(liolaemus,c("ctenads","pymsom","pymzap",
    "pympal","pympun"))
iguanids<-read.csv(file=
    "https://datadryad.org/bitstream/handle/10255/dryad.169644/iguanids.csv",
    row.names=1)
liol.data<-iguanids[liolaemus$tip.label,c(1,3)]
liol.data$TAL<-as.numeric(liol.data$TAL)
liol.data$residTAL<-
    phyl.resid(liolaemus,x=as.matrix(liol.data[,1,
    drop=FALSE]),Y=as.matrix(liol.data[,2,
    drop=FALSE]))$resid
liolaemus<-paintSubTree(liolaemus,
    Ntip(liolaemus)+1,"1")
object<-phyloScattergram(liolaemus,
    liol.data[,c(1,3)],plot=FALSE)
## Computing multidimensional phylogenetic scatterplot matrix...
object<-setMap(object,invert=TRUE)
plot(object,colors=setNames("blue",1),
    ftype="off")

plot of chunk unnamed-chunk-2

Neat.

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