Graphical display of phylogeny and traits
This function represents traits onto the tips of a phylogeny. Plotted objects
must be valid phylo4d objects (implemented by the
phylobase package). Current version allows plotting of a tree and one
or more quantitative traits (possibly containing missing data, represented by
an 'x').
table.phylo4d(x, treetype = c("phylogram", "cladogram"),
symbol = c("circles", "squares", "colors"), repVar = 1:ncol(tdata(x, type
= "tip")), center = TRUE, scale = TRUE, legend = TRUE, grid = TRUE,
box = TRUE, show.tip.label = TRUE, show.node.label = TRUE,
show.var.label = TRUE, ratio.tree = 1/3, font = 3,
tip.label = tipLabels(x), var.label = colnames(tdata(x, type = "tip")),
cex.symbol = 1, cex.label = 1, cex.legend = 1, pch = 20,
col = heat.colors(100), coord.legend = NULL, ...)x |
a phylo4d object |
treetype |
the type of tree to be plotted ("phylogram" or "cladogram") |
symbol |
the type of symbol used to represent data ("circles", "squares", or "colors") |
repVar |
the numerical index of variables to be plotted |
center |
a logical stating whether variables should be centred (TRUE, default) or not (FALSE) |
scale |
a logical stating whether variables should be scaled (TRUE, default) or not (FALSE) |
legend |
a logical stating whether a legend should be added to the plot (TRUE) or not (FALSE, default) |
grid |
a logical stating whether a grid should be added to the plot (TRUE, default) or not (FALSE) |
box |
a logical stating whether a box should be added around the plot (TRUE, default) or not (FALSE) |
show.tip.label |
a logical stating whether tip labels should be printed (TRUE, default) or not (FALSE) |
show.node.label |
a logical stating whether node labels should be printed (TRUE, default) or not (FALSE) |
show.var.label |
a logical stating whether labels of variables should be printed (TRUE, default) or not (FALSE) |
ratio.tree |
the proportion of width of the figure occupied by the tree |
font |
an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, default), or 4 (bold italic). |
tip.label |
a character vector giving the tip labels |
var.label |
a character vector giving the labels of variables |
cex.symbol |
a numeric giving the factor scaling the symbols |
cex.label |
a numeric giving the factor scaling all labels |
cex.legend |
a numeric giving the factor scaling the legend |
pch |
is |
col |
is |
coord.legend |
an optional list with two components 'x' and 'y'
indicating the lower-left position of the legend. Can be set to
|
... |
further arguments to be passed to plot methods from |
The plot of phylogenies is performed by a call to
plot.phylo from the ape package. Hence, many of the
arguments of plot.phylo can be passed to
table.phylo4d, through the ... argument, but their names must be
complete.
For large trees, consider using bullseye.
The function table.phylo4d is based on former plot method for
phylo4d objects from the phylobase package. It replaces
the deprecated ade4 functions symbols.phylog and
table.phylog.
Thibaut Jombart tjombart@imperial.ac.uk
The phylo4d class for storing
phylogeny+data.
For large trees, consider using bullseye.
plot.phylo from the ape package.
An alternative (deprecated) representation is available from
dotchart.phylog.
if(require(ape) & require(phylobase) & require(ade4)){
## simulated data
tr <- rtree(20)
dat <- data.frame(a = rnorm(20), b = scale(1:20), c=runif(20,-2,2) )
dat[3:6, 2] <- NA # introduce some NAs
obj <- phylo4d(tr, dat) # build a phylo4d object
table.phylo4d(obj) # default scatterplot
table.phylo4d(obj,cex.leg=.6, use.edge.length=FALSE) # customized
table.phylo4d(obj,treetype="clad", show.node=FALSE, cex.leg=.6,
use.edge.length=FALSE, edge.color="blue", edge.width=3) # more customized
## teleost fishes data
data(mjrochet)
temp <- read.tree(text=mjrochet$tre) # make a tree
mjr <- phylo4d(x=temp,tip.data=mjrochet$tab) # male a phylo4d object
table.phylo4d(mjr,cex.lab=.5,show.node=FALSE,symb="square")
## lizards data
data(lizards)
liz.tr <- read.tree(tex=lizards$hprA) # make a tree
liz <- phylo4d(liz.tr, lizards$traits) # make a phylo4d object
table.phylo4d(liz)
## plotting principal components
liz.pca1 <- dudi.pca(lizards$traits, scannf=FALSE, nf=2) # PCA of traits
myPC <- phylo4d(liz.tr, liz.pca1$li) # store PC in a phylo4d object
varlab <- paste("Principal \ncomponent", 1:2) # make labels for PCs
table.phylo4d(myPC, ratio=.8, var.lab=varlab) # plot the PCs
add.scatter.eig(liz.pca1$eig,2,1,2,posi="topleft", inset=c(0,.15))
title("Phylogeny and the principal components")
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