njplot {ade4}R Documentation

Phylogeny and trait of bacteria

Description

This data set describes the phylogeny of 36 bacteria as reported by Perrière and Gouy (1996). It also gives the GC rate corresponding to these 36 species.

Usage

data(njplot)

Format

njplot is a list containing the 2 following objects:

tre
is a character string giving the fission tree in Newick format.
tauxcg
is a numeric vector that gives the CG rate of the 36 species.

Source

Data were obtained by Manolo Gouy mgouy@biomserv.univ-lyon1.fr

References

Perrière, G. and Gouy, M. (1996) WWW-Query : an on-line retrieval system for biological sequence banks. Biochimie, 78, 364–369.

Examples

data(njplot)
njplot.phy <- newick2phylog(njplot$tre)
par(mfrow = c(2,1))
tauxcg0 <- njplot$tauxcg - mean(njplot$tauxcg)
symbols.phylog(njplot.phy, squares = tauxcg0)
symbols.phylog(njplot.phy, circles = tauxcg0)
par(mfrow = c(1,1))

Worked out examples


> library(ade4)
> ### Name: njplot
> ### Title: Phylogeny and trait of bacteria
> ### Aliases: njplot
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(njplot)
> njplot.phy <- newick2phylog(njplot$tre)
> par(mfrow = c(2,1))
> tauxcg0 <- njplot$tauxcg - mean(njplot$tauxcg)
> symbols.phylog(njplot.phy, squares = tauxcg0)
> symbols.phylog(njplot.phy, circles = tauxcg0)
> par(mfrow = c(1,1))
> 
> 
> 
> 

[Package ade4 Index]