ade4 (version 1.2-2)

symbols.phylog: Representation of a quantitative variable in front of a phylogenetic tree

Description

symbols.phylog draws the phylogenetic tree and represents the values of the variable by symbols (squares or circles) which size is proportional to value. White symbols correspond to values which are below the mean, and black symbols correspond to values which are over. dotchart.phylog represents the phylogenetic tree and draws a Cleveland dot plot of the variable.

Usage

symbols.phylog(phylog, circles, squares, csize = 1, clegend = 1,
 sub = "", csub = 1, possub = "topleft")
dotchart.phylog(phylog, values, ceti = 1, cdot = 1, ...)

Arguments

phylog

an object of class phylog

circles

a vector giving the radii of the circles

squares

a vector giving the length of the sides of the squares

values

a vector giving the position in a dotplot

csize

a size coefficient for symbols

ceti

a character size for the legend of the dot plot, used with par("cex")*ceti

cdot

a character size for plotting the points of the dot plot, used with par("cex")*cdot

clegend

a character size for the legend used by par("cex")*clegend

sub

a string of characters to be inserted as legend

csub

a character size for the legend, used with par("cex")*csub

possub

a string of characters indicating the sub-title position ("topleft", "topright", "bottomleft", "bottomright")

...

further arguments passed to or from other methods

See Also

table.phylog for many variables

Examples

data(mjrochet)
mjrochet.phy <- newick2phylog(mjrochet$tre)
tab0 <- data.frame(scalewt(log(mjrochet$tab)))
par(mfrow=c(3,2))
for (j in 1:6) {
    w <- tab0[,j]
    symbols.phylog(phylog = mjrochet.phy, w, csi = 1.5, cleg = 1.5,
     sub = names(tab0)[j], csub = 3)
}
par(mfrow=c(1,1))

par(mfrow=c(2,3))
for (j in 1:6) {
    w <- tab0[,j]
    dotchart.phylog(mjrochet.phy, w, cdot=1.5,
        sub=names(tab0)[j],csub=3,cnodes=2,ceti=1.5)
}
par(mfrow=c(1,1))