ggtortoises {ade4}R Documentation

Microsatellites of Galapagos tortoises populations

Description

This data set gives genetic relationships between Galapagos tortoises populations with 10 microsatellites.

Usage

data(ggtortoises)

Format

ggtortoises is a list of 6 components.

area
is a data frame designed to be used in area.plot function.
ico
is a list of three pixmap icons representing the tortoises morphotypes.
pop
is a data frame containing meta informations about populations.
misc
is a data frame containing the coordinates of the island labels.
loc
is a numeric vector giving the number of alleles by marker.
tab
is a data frame containing the number of alleles by populations for 10 microsatellites.

Source

M.C. Ciofi, C. Milinkovitch, J.P. Gibbs, A. Caccone, and J.R. Powell (2002) Microsatellite analysis of genetic divergence among populations of giant galapagos tortoises. Molecular Ecology 11: 2265-2283.

References

M.C. Ciofi, C. Milinkovitch, J.P. Gibbs, A. Caccone, and J.R. Powell (2002) Microsatellite analysis of genetic divergence among populations of giant galapagos tortoises. Molecular Ecology 11: 2265-2283.

See a data description at http://pbil.univ-lyon1.fr/R/pps/pps069.pdf (in French).

Examples

if(require(pixmap, quiet=TRUE)){
	data(ggtortoises)
	a1 <- ggtortoises$area
	area.plot(a1)
	rect(min(a1$x), min(a1$y), max(a1$x), max(a1$y), col = "lightblue")
	invisible(lapply(split(a1, a1$id), function(x) polygon(x[, -1],col = "white")))
	s.label(ggtortoises$misc, grid=FALSE,include.ori=FALSE,addaxes=FALSE,add.p=TRUE)
	listico <- ggtortoises$ico[as.character(ggtortoises$pop$carap)]
	s.logo(ggtortoises$pop,listico,add.p=TRUE)
}

Worked out examples


> library(ade4)
> ### Name: ggtortoises
> ### Title: Microsatellites of Galapagos tortoises populations
> ### Aliases: ggtortoises
> ### Keywords: datasets
> 
> ### ** Examples
> 
> if(require(pixmap, quiet=TRUE)){
+ 	data(ggtortoises)
+ 	a1 <- ggtortoises$area
+ 	area.plot(a1)
+ 	rect(min(a1$x), min(a1$y), max(a1$x), max(a1$y), col = "lightblue")
+ 	invisible(lapply(split(a1, a1$id), function(x) polygon(x[, -1],col = "white")))
+ 	s.label(ggtortoises$misc, grid=FALSE,include.ori=FALSE,addaxes=FALSE,add.p=TRUE)
+ 	listico <- ggtortoises$ico[as.character(ggtortoises$pop$carap)]
+ 	s.logo(ggtortoises$pop,listico,add.p=TRUE)
+ }
> 
> 
> 
> 

[Package ade4 Index]