View source: R/plotTree.datamatrix.R
plotTree.datamatrix | R Documentation |
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.
plotTree.datamatrix(tree, X, ...)
plotFanTree.wTraits(tree, X, type=c("arc","fan"), ...)
tree |
an object of class |
X |
a data frame with columns as factors for |
type |
plot type for |
... |
optional arguments. |
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.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
dotTree
, phylo.heatmap
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
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