plot.traitMedusa.model {motmot} | R Documentation |
Tree plotting for rates
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 |
y |
A matrix of trait values. |
... |
Other functions to pass to |
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)
[Package motmot version 2.1.3 Index]