phytools: contMap – R documentation

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contMap

Map continuous trait evolution on the tree

Description

Function plots a tree with a mapped continuous character. The mapping is accomplished by estimating states at internal nodes using ML with fastAnc, and then interpolating the states along each edge using equation [2] of Felsenstein (1985).

errorbar.contMap adds error bars to an existing plot.

Usage

contMap(tree, x, res=100, fsize=NULL, ftype=NULL, lwd=4, legend=NULL,
   lims=NULL, outline=TRUE, sig=3, type="phylogram", direction="rightwards", 
   plot=TRUE, ...)
## S3 method for class 'contMap'
plot(x, ...)
errorbar.contMap(obj, ...)

Arguments

`tree`	object of class `"phylo"`.
`x`	a numerical vector of phenotypic trait values for species. `names(x)` should contain the species names and match `tree$tip.label`. Or, for `plot.contMap`, an object of class `"contMap"`.
`res`	resolution for gradient plotting. Larger numbers (to a point) indicate a finer (smoother) gradient.
`fsize`	relative font size - can be a vector of length 2 in which the first element gives the font size for the tip labels & the second element giving the font size for the legend.
`ftype`	font type - see options in `plotSimmap`. As with `fsize`, this can be a vector with the second element giving font type for the legend.
`lwd`	line width for branches. Can be a single integer number or a vector. In the latter case, the second number will be taken to be the desired legend width.
`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.
`lims`	range for the color map. By default, this will be `c(min(x),max(x))`, and should always include this range.
`outline`	logical value indicating whether or not to outline the branches of the tree in black.
`sig`	the number of decimal places to show on the legend limits.
`type`	type of plot desired. Options are `"phylogram"` for a rightward square phylogram; and `"fan"` for a circular phylogram.
`direction`	plotting direction for `type="phylogram"`.
`plot`	logical value indicating whether or not to plot the tree. If `plot=FALSE` then an object of class `"contMap"` will be returned without plotting.
`obj`	object of class `"contMap"`.
`...`	optional arguments for `plot.contMap` which include all the arguments of `contMap` except for `tree`, `x`, `res`, and `lims`. Also `method`, `"fastAnc"`, `"anc.ML"`, or `"user"` (for user-supplied states) specifying which function to use for ancestral state estimation; `hold` specifies whether or not to hold output to graphical device before plotting (defaults to `hold=TRUE`); and `anc.states` a vector containing some or multiple ancestral user-supplied ancestral states at nodes. Some other plotting arguments, such as `xlim` and `ylim`, may also work. Optional arguments for `errorbar.contMap` include `x`, a vector containing the original trait values mapped onto the tree (otherwise these will be obtained from `obj`), `scale.by.ci`, a logical argument (defaulting to `TRUE`) that determines whether or not the length of the error bars will be scaled by the CI width, and `lwd`, which detemines the line width of the plotted error bars.

Value

Plots a tree. An object of class "contMap" is returned invisibly.

errorbar.contMap adds colorful error bars to a plotted tree.

Author(s)

Liam Revell liam.revell@umb.edu

References

Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist, 125, 1-15.

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 data from Garland et al. (1992)
data(mammal.tree)
data(mammal.data)
## extract character of interest
ln.bodyMass<-log(setNames(mammal.data$bodyMass,
    rownames(mammal.data)))
## create "contMap" object
mammal.contMap<-contMap(mammal.tree,
    ln.bodyMass,plot=FALSE,res=200)
## change color scheme
mammal.contMap<-setMap(mammal.contMap,
    c("white","#FFFFB2","#FECC5C","#FD8D3C",
    "#E31A1C"))
plot(mammal.contMap,fsize=c(0.7,0.8),
    leg.txt="log(body mass)")
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