densityTree {phytools}

Plots a posterior sample of trees

Description

Functions plots a posterior sample of trees, including with mapped discrete characters.

make.transparent is used internally and converts a color to transparent with a certain user-specified alpha level.

Usage

densityTree(trees, colors="blue", alpha=NULL, method="plotTree", 
   fix.depth=FALSE, use.edge.length=TRUE, compute.consensus=TRUE, 
   use.gradient=FALSE, show.axis=TRUE, ...)
make.transparent(color, alpha)

Arguments

trees

an object of class "multiPhylo" or "multiSimmap".

colors

a color or a named vector of colors in which names correspond to mapped states in an object of class "multiSimmap".

alpha

transparency level for plotted trees which is passed to internally used function, make.transparent. (0 is fully transparent, which 1 is fully opaque.) By default will be one divided by the number of trees.

method

plotting method to be used internally. Can be "plotTree" or "plotSimmap".

fix.depth

logical value indicating whether or not to plot trees with a fixed depth or to permit plotted trees to have different depths.

use.edge.length

logical value indicating whether to use the edge lengths of the input tree. Defaults to use.edge.length=TRUE unless any input tree edge lengths are NULL.

compute.consensus

logical value indicating whether or not to use the tip order from a consensus tree. (Defaults to compute.consensus=TRUE Defaulted to FALSE in earlier version of this function.)

use.gradient

logical value indicating whether to plot all trees slightly offset using a rainbow color gradient. (Defaults to use.gradient=FALSE.)

show.axis

logical value indicating whether or not to include a horizontal axis in the plot.

...

arguments to be passed to plotTree or plotSimmap. Some may be ignored if they are incompatible with the method.

color

in make.transparent, the color (or colors in a vector) to render transparent.

Value

Function creates a plot.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.