phytools: plotTree.wBars – R documentation

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plotTree.wBars

Plot a tree with bars at the tips

Description

plotTree.wbars plots a phylogeny in phylogram or fan style with bars at the tips representing the values for a phenotypic trait.

plotTree.barplot creates a split plot in which a right-facing phylogram is on the left, and a bar plot is shown on the right.

plotTree.boxplot creates a split plot in which a right-facing phylogram is on the left, and a box plot is shown on the right.

Usage

plotTree.wBars(tree, x, scale=NULL, width=NULL, type="phylogram", 
   method="plotTree", tip.labels=FALSE, col="grey", border=NULL, 
   ...)
plotTree.barplot(tree, x, args.plotTree=list(), args.barplot=list(), 
	...)
plotTree.boxplot(tree, x, args.plotTree=list(), args.boxplot=list())

Arguments

`tree`	an object of class `"phylo"`.
`x`	a named vector or matrix of trait values. For `plotTree.boxplot`, the names should repeat for multiple observations per species. For `plotTree.boxplot` `x` can also be supplied as a formula, though in that case the factor levels need to be provided in a valid cladewise order of the tips in `tree`. This order doesn't need to correspond with the current order of the tip labels. For `plotTree.barplot` `x` can be a matrix (or a data frame) in which columns are the values of multiple traits to be simultaneously plotted on the tree.
`scale`	scaling factor for the tip bars (relative to the total tree height). If left as `NULL` a reasonable scaling factor is computed automatically.
`width`	width of the tip bars.
`type`	plot type. Can be `"phylogram"` or `"fan"`.
`method`	plotting method to use. Can be `"plotTree"` (for `plotTree`) or `"plotSimmap"` (for `plotSimmap`).
`tip.labels`	argument indicating whether or not tip labels should be plotted. Defaults to `tip.labels=FALSE`.
`col`	colors of the plotted bars. Can be a single value or a vector with length equal to the number of tips in the tree.
`border`	single value specifying the color of the border for the plotted bars. Defaults to `border=NULL`, which means that black borders will be plotted.
`args.plotTree`	in `plotTree.barplot`, arguments to be passed to `plotTree`.
`args.barplot`	in `plotTree.barplot`, arguments to be passed to `barplot`.
`args.boxplot`	in `plotTree.boxplot`, arguments to be passed to `boxplot`.
`...`	optional arguments to be passed to `plotTree` or `plotSimmap` in the case of `plotTree.wBars`. For `plotTree.barplot`, the only optional argument is `add`. Generally this should not be used; however it can be used to tell the function to draw the tree & barplot, respectively, in the next two open plotting devices - rather than creating a table of figures in the current plotting device.

Value

Plots a tree with an associated bar plot for a continuously valued character at the tips.

Author(s)

Liam Revell liam.revell@umb.edu

References

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

Examples

## load data from Mahler et al. (2010)
data(anoletree)
data(anole.data)
## extract overall body size (SVL)
svl<-setNames(anole.data$SVL,rownames(anole.data))
## plotTree.wBars
plotTree.wBars(anoletree,svl,type="fan",scal=0.5)
par(mar=c(5.1,4.1,4.1,2.1))
## plotTree.barplot
plotTree.barplot(anoletree,exp(svl),
    args.plotTree=list(fsize=0.5),
    args.barplot=list(xlab="SVL (mm)"))
	
## load vertebrate tree and data
data(vertebrate.tree)
data(vertebrate.data)
## plotTree.barplot
options(scipen=3) ## change sci-notation
plotTree.barplot(vertebrate.tree,
	setNames(vertebrate.data$Mass,
	rownames(vertebrate.data)),
	args.barplot=list(log="x",
	xlab="mass (kg)",
	xlim=c(0.01,500000),
	col=palette()[4]))
options(scipen=0)

## reset par to defaults
par(mfrow=c(1,1),mar=c(5.1,4.1,4.1,2.1))

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19