Monday, May 27, 2013

Circular trees in densityMap and contMap

In an earlier post I showed how plotSimmap(...,type="fan") could be used to plot densityMap or contMap style plots using the object of class "densityMap" or "contMap" returned invisibly by each function, respectively.

Well, I have now build this directly into contMap & densityMap (and the S3 generic plot for objects of class "densityMap" and "contMap"). Check it out:

> require(phytools)
Loading required package: phytools
> packageVersion("phytools")
[1] ‘0.2.76’
> contMap(tree,x,type="fan",fsize=0.9)
> X<-densityMap(mtrees,outline=TRUE,fsize=0.9)
sorry - this might take a while; please be patient

Argh - way too cluttered. Let's try a circular tree instead!

> class(X)
[1] "densityMap"
> plot(X,type="fan",fsize=0.9,outline=TRUE)

Since these updates involved changes to a number of methods in phytools - the best bet is to update to the latest non-CRAN phytools build (phytools 0.2-76).

That's it.

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