trait.plot: Plot a Phylogeny and Traits

In diversitree: Comparative 'Phylogenetic' Analyses of Diversification

Plot a Phylogeny and Traits

Description

Plot a phylogeny and label the tips with traits. This function is experimental, and may change soon. Currently it can handle discrete-valued traits and two basic tree shapes.

Usage

trait.plot(tree, dat, cols, lab=names(cols), str=NULL, 
           class=NULL, type="f", w=1/50, 
           legend=length(cols) > 1, cex.lab=.5, 
           font.lab=3, cex.legend=.75, margin=1/4, 
           check=TRUE, quiet=FALSE, ...)

Arguments

tree	Phylogenetic tree, in ape format.
dat	A data.frame of trait values. The row names must be the same names as the tree (tree$tip.label), and each column contains the states (0, 1, etc., or NA). The column names must give the trait names.
cols	A list with colors. Each element corresponds to a trait and must be named so that all names appear in names(dat). Each of these elements is a vector of colors, with length matching the number of states for that trait. Traits will be plotted in the order given by cols.
lab	Alternative names for the legend (perhaps longer or more informative). Must be in the same order as cols.
str	Strings used for the states in the legend. If NULL (the default), the values in dat are used.
class	A vector along phy$tip.label giving a higher level classification (e.g., genus or family). No checking is done to ensure that such classifications are not polyphyletic.
type	Plot type (same as type in ?plot.phylo). Currently only f (fan) and p (rightwards phylogram) are implemented.
w	Width of the trait plot, as a fraction of the tree depth.
legend	Logical: should a legend be plotted?
cex.lab, font.lab	Font size and type for the tip labels.
cex.legend	Font size for the legend.
margin	How much space, relative to the total tree depth, should be reserved when plotting a higher level classification.
check	When TRUE (by default), this will check that the classes specified by class are monophyletic. If not, classes will be concatenated and a warning raised.
quiet	When TRUE (FALSE by default), this suppresses the warning caused by check=TRUE.
...	Additional arguments passed through to phylogeny plotting code (similar to ape's plot.phylo).

Author(s)

Richard G. FitzJohn

Examples

## Due to a change in sample() behaviour in newer R it is necessary to
## use an older algorithm to replicate the previous examples
if (getRversion() >= "3.6.0") {
  RNGkind(sample.kind = "Rounding")
}

## These are the parameters: they are a single speciation and extinction
## rate, then 0->1 (trait A), 1->0 (A), 0->1 (B) and 1->0 (B).
colnames(musse.multitrait.translate(2, depth=0))

## Simulate a tree where trait A changes slowly and B changes rapidly.
set.seed(1)
phy <- tree.musse.multitrait(c(.1, 0, .01, .01, .05, .05),
                             n.trait=2, depth=0, max.taxa=100,
                             x0=c(0,0))
## Here is the matrix of tip states (each row is a species, each column
## is a trait).
head(phy$tip.state)

trait.plot(phy, phy$tip.state,
           cols=list(A=c("pink", "red"), B=c("lightblue", "blue")))

nodes <- c("nd5", "nd4", "nd7", "nd11", "nd10", "nd8")
grp <- lapply(nodes, get.descendants, phy, tips.only=TRUE)
class <- rep(NA, 100)
for ( i in seq_along(grp) )
  class[grp[[i]]] <- paste("group", LETTERS[i])

## Now, 'class' is a vector along phy$tip.label indicating which of six
## groups each species belongs.

## Plotting the phylogeny with these groups:
trait.plot(phy, phy$tip.state,
           cols=list(A=c("pink", "red"), B=c("lightblue", "blue")),
           class=class, font=1, cex.lab=1, cex.legend=1)

## Add another state, showing values 1:3, names, and trait ordering.
tmp <- sim.character(phy, c(-.1, .05, .05, .05, -.1, .05, .05, 0.05, -.1), 
                     model="mkn", x0=1)
phy$tip.state <- data.frame(phy$tip.state, C=tmp)
trait.plot(phy, phy$tip.state,
           cols=list(C=c("palegreen", "green3", "darkgreen"),
                     A=c("pink", "red"), B=c("lightblue", "blue")),
           lab=c("Animal", "Vegetable", "Mineral"),
           str=list(c("crane", "toad", "snail"), c("kale", "carrot"), 
                    c("calcite", "beryl")))

## Rectangular/phylogram plot with groups.
trait.plot(ladderize(phy, right=FALSE), phy$tip.state, type="p",
           cols=list(A=c("pink", "red"), B=c("lightblue", "blue"),
                     C=c("palegreen", "green3", "darkgreen")),
           class=class, font=1, cex.lab=1)

diversitree documentation built on Oct. 2, 2024, 9:13 a.m.