ggtortoises: Microsatellites of Galapagos tortoises populations

In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

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 with the following components:

area

a data frame designed to be used in the area.plot function

ico

a list of three pixmap icons representing the tortoises morphotypes

pop

a data frame containing meta informations about populations

misc

a data frame containing the coordinates of the island labels

loc

a numeric vector giving the number of alleles by marker

tab

a data frame containing the number of alleles by populations for 10 microsatellites

Spatial

an object of the class SpatialPolygons of sp, containing the map

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/pdf/pps069.pdf (in French).

Examples

if(requireNamespace("pixmap", quietly=TRUE)) {
  data(ggtortoises)
  
  if(adegraphicsLoaded()) {
    if(requireNamespace("sp", quietly = TRUE)) {
      g1 <- s.logo(ggtortoises$pop, ggtortoises$ico[as.character(ggtortoises$pop$carap)], 
        Sp = ggtortoises$Spatial, pbackground.col = "lightblue", pSp.col = "white", 
        pgrid.draw = FALSE, ppoints.cex = 0.5)
      g1 <- s.label(ggtortoises$misc, pgrid.draw = FALSE, porigin.include = FALSE, 
        paxes.draw = FALSE, add = TRUE)
    }

  } else {    
  	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)
  }
}

ade4 documentation built on Feb. 16, 2023, 7:58 p.m.