phytools: densityMap – R documentation

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densityMap

Plot posterior density of stochastic mapping on a tree

Description

Function plots a tree with the posterior density for a mapped character from stochastic character mapping on the tree. Since the mapped value is the probability of being in state "1", only binary [0,1] characters are allowed.

Usage

densityMap(trees, res=100, fsize=NULL, ftype=NULL, lwd=3, check=FALSE,
   legend=NULL, outline=FALSE, type="phylogram", direction="rightwards",
   plot=TRUE, ...)
## S3 method for class 'densityMap'
plot(x, ...)

Arguments

`trees`	set of phylogenetic trees in a modified `"multiPhylo"` object. Values for a two-state discrete character are mapped on the tree. See `make.simmap` and `read.simmap` for details.
`res`	resolution for gradient plotting. Larger numbers indicate a finer (smoother) gradient.
`fsize`	relative font size - can be a vector with the second element giving the font size for the legend.
`ftype`	font type - see options in `plotSimmap`. As with `fsize`, can be a vector with the second element giving font type for the legend.
`lwd`	line width for branches. If a vector of two elements is supplied, the second element will be taken to be the desired width of the legend bar.
`check`	check to make sure that the topology and branch lengths of all phylogenies in `trees` are equal.
`legend`	if `FALSE` no legend is plotted; if a numeric value, it gives the length of the legend in units of branch length. Default is 0.5 times the total tree length.
`outline`	logical value indicating whether or not to outline the branches of the tree in black.
`type`	type of plot desired. Options are `"phylogram"` for a rightward square phylogram; and `"fan"` for a circular phylogram.
`plot`	logical value indicating whether or not to plot the tree. If `plot=FALSE` then an object of class `"densityMap"` will be returned without plotting.
`direction`	plotting direction for `type="phylogram"`.
`x`	for `plot.densityMap`, an object of class `"densityMap"`.
`...`	optional arguments for `plot.densityMap`. These include all the arguments of `densityMap` except `trees` and `res`. Additional optional arguments include `mar` (margins), `offset` (tip label offset: in units of the edge length or character widths, as in `plotSimmap`), and `hold` (whether or not to use `dev.hold` to hold output to graphical device before plotting; defaults to `hold=TRUE`). Also, the argument `states` can be used to 'order' the states on the probability axis (that is, which state should correspond to a posterior probability of 0 or 1). Some other plotting arguments, such as `xlim` and `ylim`, may also work.

Value

Plots a tree and returns an object of class "densityMap" invisibly.

Author(s)

Liam Revell liam.revell@umb.edu

References

Bollback, J. P. 2006. Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.

Huelsenbeck, J. P., R. Neilsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Systematic Biology, 52, 131-138.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

Revell, L. J. 2013. Two new graphical methods for mapping trait evolution on phylogenies. Methods in Ecology and Evolution, 4, 754-759.

Examples

## load tree and data from Revell & Collar (2009)
data(sunfish.tree)
data(sunfish.data)
## extract discrete character (feeding mode)
fmode<-setNames(sunfish.data$feeding.mode,
     rownames(sunfish.data))
## do stochastic mapping
smap.trees<-make.simmap(sunfish.tree,fmode,model="ER",
     nsim=100)
## compute "densityMap" object
sunfish.dmap<-densityMap(smap.trees,plot=FALSE,
	res=50) ## res should be higher
## plot density map
plot(sunfish.dmap,lwd=5,outline=TRUE)
par(mar=c(5.1,4.1,4.1,2.1)) ## reset margins to default

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19