spider (version 1.5.0)

ordinDNA: Calculates a Principal Components Ordination of genetic distances

Description

Calculates Principical Coonrdinates Analysis on a matrix of genetic distances and plots an ordination of the first two major axes.

Usage

ordinDNA(distobj, sppVector, ...)

Arguments

distobj

A distance matrix.

sppVector

The species vector (see sppVector).

...

Other arguments to be passed to plot.ordinDNA.

Value

Plots an ordination of the first two major axes showing the positions of each individual (squares), the centroid of each species (circular bullet and name of species), and the variation in the species (large circle, the radius of which is the distance to the furthest individual from the centroid).

Additionally returns a list of class "ordinDNA" with the following elements:

pco

Output of the Principal Coordinates Analysis.

sppVector

Character vector giving the species vector.

Details

This function is a wrapper for cmdscale, which performs a Principal Coordinates Analysis on the distance matrix given. In addition, it plots an ordination of the genetic distance matrix given, showing the relative distance between each of the species in the dataset. It is presented as an alternative to the neighbour-joining trees which are frequently used for the visualisation of DNA barcoding data. NJ trees show hypotheses of relationships, which are inappropriate for the questions usally asked in DNA barcoding studies.

The distance between the centroids of the clusters are roughly proportional to the genetic distances between the species. NOTE: it is important to remember that the plot shows only one plane of a multi-dimensional space. Species with overlapping circles are not necessarily conspecific. Further exploration is required.

See Also

cmdscale, plot.ordinDNA

Examples

# NOT RUN {

data(dolomedes)
doloDist <- ape::dist.dna(dolomedes)
doloSpp <- substr(dimnames(dolomedes)[[1]], 1, 5)

doloOrd <- ordinDNA(doloDist, doloSpp)
doloOrd

# }