ggtortoises: Microsatellites of Galapagos tortoises populations

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

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/pdf/pps069.pdf (in French).

Examples

if(requireNamespace("pixmap", quiet=TRUE)) {
  data(ggtortoises)
  
  if(adegraphicsLoaded()) {
    if(requireNamespace("sp", quiet = TRUE)) {
      g1 <- s.logo(ggtortoises$pop, ggtortoises$ico[as.character(ggtortoises$pop$carap)], 
        Sp = ggtortoises$Spatial, pback.col = "lightblue", pSp.col = "white", pgrid.draw = FALSE,
        ppoints.cex = 0.5)
      g1 <- s.label(ggtortoises$misc, pgrid.draw = FALSE, porigin.include = FALSE, paxes.draw = F, 
        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 May 2, 2019, 5:50 p.m.