plotTree.datamatrix: Plot a tree with a discrete (or continuous) character data...

In liamrevell/phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

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"), ...)

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.

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.

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.

See Also

dotTree, phylo.heatmap

Examples

data("liolaemid.data")
data("liolaemid.tree")
liolaemid.data[liolaemid.tree$tip.label,]->liolaemid.data
colors<-list(
  c("blue","white","red"),
  terrain.colors(n=10),
  setNames(c("#F0EAD6","#DF536B"),c("O","V")))
cols<-plotFanTree.wTraits(liolaemid.tree,
  liolaemid.data[,3:1],lwd=12,colors=colors,ftype="off",
  spacer=0)
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)
par(mar=c(5.1,4.1,4.1,2.1)) ## reset margins to default

liamrevell/phytools documentation built on April 8, 2024, 9:59 p.m.