R: Microsatellites of Galapagos tortoises populations

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 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)
      }
    }

[Package ade4 version 1.7-18 Index]