ade4: njplot – R documentation

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njplot

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 manolo.gouy@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))

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