Friday, September 19, 2014

Small update to fancyTree method "phenogram95" to permit control of shading

Today I made what amounts to quite a small update to the "phenogram95" method in the function fancyTree. This function plots a 95% high probability density region around a reconstructed 'traitgram' (i.e., a projection of the tree into a space defined by one phenotypic trait on the vertical axis and type since the root on the horizontal axis). This visual effect is accomplished by increasingly transparently shaded lines. The update permits user control of transparency shading which, at present, is completely arbitrary. Here's what that looks like:

library(phytools)
packageVersion("phytools")
## [1] '0.4.35'
## simulate a tree & data
tree<-pbtree(n=26,tip.label=LETTERS,scale=1)
x<-fastBM(tree)
## create 95% traitgram
fancyTree(tree,x=x,type="phenogram95",tlim=c(1,25)) ## light shading

plot of chunk unnamed-chunk-1

fancyTree(tree,x=x,type="phenogram95",tlim=c(10,50)) ## dark shading

plot of chunk unnamed-chunk-1

Transparency upper & lower limits should be specified on the interval (0,99).

For the latest 'bleeding edge' version of phytools with this update see the phytools page. For more information on this and other plotting methods, check out my recent book chapter.

That's it!

1 comment:

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