symbols.phylog {ade4}R Documentation

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
S├ębastien Ollier ollier@biomserv.univ-lyon1.fr

See Also

table.phylog and dotchart.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))

Worked out examples


> library(ade4)
> ### Name: symbols.phylog
> ### Title: Representation of a quantitative variable in front of a
> ###   phylogenetic tree
> ### Aliases: symbols.phylog
> ### Keywords: hplot
> 
> ### ** 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))
> 
> 
> 
> 

[Package ade4 Index]