markChanges: Add marked changes to a plotted tree with mapped discrete...

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

Add marked changes to a plotted tree with mapped discrete character

Description

Adds the reconstructed changes to a plotted tree with a stochastically mapped discrete character.

Usage

markChanges(tree, colors=NULL, cex=1, lwd=2, plot=TRUE)

Arguments

tree	an object of class "simmap".
colors	a named vector of colors used to plot the stochastically mapped character on the tree.
cex	expansion factor for line height.
lwd	line width.
plot	logical value indicating whether the changes should be plotted or not.

Value

This function returns (invisibly) a matrix containing the x & y coordinates of the marked changes on the plotted tree.

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

plotSimmap

Examples

## load tree and data from Revell & Collar (2009)
data(sunfish.tree)
data(sunfish.data)
## extract discrete character (feeding mode)
fmode<-setNames(sunfish.data$feeding.mode,
  rownames(sunfish.data))
## fit model
er_model<-fitMk(sunfish.tree,fmode,model="ER",
  pi="fitzjohn")
## generate single stochastic map
sunfish_smap<-simmap(er_model,nsim=1)
## plot stochastic map & mark changes
cols<-setNames(c("blue","red"),levels(fmode))
plot(sunfish_smap,cols,ftype="i")
markChanges(sunfish_smap,colors=cols,lwd=6)
par(mar=c(5.1,4.1,4.1,2.1))

phytools documentation built on June 22, 2024, 10:39 a.m.