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.
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())an object of class "phylo".
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.
scaling factor for the tip bars (relative to the total tree height). If left as NULL a reasonable scaling factor is computed automatically.
width of the tip bars.
plot type. Can be "phylogram" or "fan".
plotting method to use. Can be "plotTree" (for plotTree) or "plotSimmap" (for plotSimmap).
argument indicating whether or not tip labels should be plotted. Defaults to tip.labels=FALSE.
colors of the plotted bars. Can be a single value or a vector with length equal to the number of tips in the tree.
single value specifying the color of the border for the plotted bars. Defaults to border=NULL, which means that black borders will be plotted.
in plotTree.barplot, arguments to be passed to plotTree.
in plotTree.barplot, arguments to be passed to barplot.
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.
Plots a tree with an associated bar plot for a continuously valued character at the tips.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.