ade4: symbols.phylog – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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.

Usage

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

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
`csize`	a size coefficient for symbols
`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")

Author(s)

Daniel Chessel
Sébastien Ollier sebastien.ollier@u-psud.fr

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))

ade4

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release