R: Calculates a distance matrix for populations with SNP...

gl.dist.pop

R Documentation

Calculates a distance matrix for populations with SNP genotypes in a genlight object

Description

This script calculates various distances between populations based on allele frequencies (SNP genotypes) or frequency of presences in PA (SilicoDArT) data

Usage

gl.dist.pop(
  x,
  as.pop = NULL,
  method = "euclidean",
  scale = FALSE,
  type = "dist",
  plot.display = TRUE,
  plot.theme = theme_dartR(),
  plot.colors = NULL,
  plot.file = NULL,
  plot.dir = NULL,
  verbose = NULL
)

Arguments

`x`	Name of the genlight containing [required].
`as.pop`	Temporarily assign another locus metric as the population for the purposes of deletions [default NULL].
`method`	Specify distance measure [default euclidean].
`scale`	If TRUE and method='Euclidean', the distance will be scaled to fall in the range [0,1] [default FALSE].
`type`	Specify the type of output, dist or matrix [default dist]
`plot.display`	If TRUE, resultant plots are displayed in the plot window [default TRUE].
`plot.theme`	Theme for the plot. See Details for options [default theme_dartR()].
`plot.colors`	List of two color names for the borders and fill of the plots [default c("#2171B5","#6BAED6")].
`plot.file`	Name for the RDS binary file to save (base name only, exclude extension) [default NULL]
`plot.dir`	Directory to save the plot RDS files [default as specified by the global working directory or tempdir()]
`verbose`	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Details

The distance measure can be one of 'euclidean', 'fixed-diff', 'reynolds', 'nei' and 'chord'. Refer to the documentation of functions in https://doi.org/10.1101/2023.03.22.533737 for algorithms and definitions.

Value

An object of class 'dist' giving distances between populations

Author(s)

author(s): Arthur Georges. Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

Examples

 
# SNP genotypes
D <- gl.dist.pop(possums.gl, method='euclidean')
D <- gl.dist.pop(possums.gl, method='euclidean',scale=TRUE)
D <- gl.dist.pop(possums.gl, method='nei')
D <- gl.dist.pop(possums.gl, method='reynolds')
D <- gl.dist.pop(possums.gl, method='chord')
D <- gl.dist.pop(possums.gl, method='fixed-diff')
#Presence-Absence data [only 10 individuals due to speed]
D <- gl.dist.pop(testset.gs[1:10,], method='euclidean')