plot.traitMedusa.model: Tree plotting for rates

In PuttickMacroevolution/motmot: Models of Trait Macroevolution on Trees

Description

Plots trees with colours based on rates of trait evolution. Also provides simple coloured plotting for trait values using the ace function in the ape library.

Usage

## S3 method for class 'traitMedusa.model'
plot(x, y = NULL, ..., reconType = "rates", palette = "hotspot.colors")

Arguments

x	Output from summary.traitMedusa.
y	A matrix of trait values.
...	Other functions to pass to plot.phylo
reconType	Colour branches according to rate shifts ("rates" - requires traitMedusaObject) or ancestral state reconstruction ("picReconstruction" - requires x).
palette	Defines the colour scheme with four options: hotspot.colors (red to blue), heat.colors (yellow to red), cool.colors (blues), combi.colors (yellows to reds and blues)

Value

Returns a data frame of colours used in plot along with rate (or ancestral state) range for each colour.

Author(s)

Gavin Thomas, Mark Puttick

See Also

transformPhylo.ML, summary.traitMedusa.

Examples

# Data and phylogeny
data(anolis.tree)
data(anolis.data)

# female SVL data
female.svl <- matrix(anolis.data[,"Female_SVL"], 
dimnames=list(rownames(anolis.data)))
input.data <- sortTraitData(phy=anolis.tree, y=female.svl, log.trait=TRUE)

# arbitarily reduce data size for speed in this example
phy.clade <- extract.clade(input.data[[1]], 182)
male.length.clade <- as.matrix(input.data[[2]][match(input.data[[1]]$tip.label, 
rownames(input.data[[2]])),])
# Identify rate shifts and print and plot results with up to one rate shifts 
# and minimum clade size of 10.
anolisSVL_MEDUSA <- transformPhylo.ML(male.length.clade, phy=phy.clade, 
model="tm1",minCladeSize=10, nSplits=1)
anolisSVL_MEDUSA_out <- summary(anolisSVL_MEDUSA, cutoff=1, AICc=FALSE)
colours <- plot(x = anolisSVL_MEDUSA_out,
reconType = "rates", type = "fan", cex=0.6, edge.width=3)

PuttickMacroevolution/motmot documentation built on June 5, 2020, 7 p.m.