phytools (version 2.4-4)

plotTree.datamatrix: Plot a tree with a discrete (or continuous) character data matrix at the tips

Description

plotTree.datamatrix plots a phylogeny next to a matrix of discrete characters. plotFanTree.wTraits plots an arc or fan style tree with discrete or continuous data at the tips.

Usage

plotTree.datamatrix(tree, X, ...)
plotFanTree.wTraits(tree, X, type=c("arc","fan"), ...)

Value

plotTree.datamatrix invisibly returns a list containing the font size, a list of the colors used for each column of the plotted data matrix, and the x-coordinate of the rightmost edge of the matrix.

plotFanTree.wTraits invisibly returns the color palette used for plotting.

Arguments

tree

an object of class "phylo".

X

a data frame with columns as factors for plotTree.datamatrix, or a matrix of data frame containing continuous and/or discrete characters for plotFanTree.wTraits.

type

plot type for plotFanTree.wTraits.

...

optional arguments.

Author

Liam Revell

References

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

See Also

dotTree, phylo.heatmap

Examples

## load data
data(liolaemid.data)
data(liolaemid.tree)

## subsample data to species in the tree
liolaemid.data<-liolaemid.data[liolaemid.tree$tip.label,]

## set colors for plotting
colors<-list(
    c("blue","white","red"),
    terrain.colors(n=10),
    setNames(c("#F0EAD6","#DF536B"),c("O","V")))

## plot fan tree with traits
cols<-plotFanTree.wTraits(liolaemid.tree,
    liolaemid.data[,3:1],lwd=12,colors=colors,ftype="off",
    spacer=0)

## add legends
legend(x=0,y=0.7*max(nodeHeights(liolaemid.tree)),
    names(colors[[3]]),lwd=8,col=colors[[3]],
    title="parity mode",bty="n",xjust=0.5,yjust=0.5)
add.color.bar(1.5*max(nodeHeights(liolaemid.tree)),cols[[2]],
    title="maximum altitude (m)",
    lims=range(liolaemid.data[,2]),digits=2,prompt=FALSE,
    x=-0.75*max(nodeHeights(liolaemid.tree)),
    y=0.2*max(nodeHeights(liolaemid.tree)),subtitle="",
    lwd=8,outline=FALSE)
add.color.bar(1.5*max(nodeHeights(liolaemid.tree)),cols[[1]],
    title="environmental temp.",
    lims=range(liolaemid.data[,3]),digits=2,prompt=FALSE,
    x=-0.75*max(nodeHeights(liolaemid.tree)),
    y=-0.15*max(nodeHeights(liolaemid.tree)),subtitle="",
    lwd=8,outline=FALSE)

## reset margins to default
par(mar=c(5.1,4.1,4.1,2.1))