dartR.base (version 0.98)

gl.sort: re-sorts genlight objects

Description

Often it is desirable to have the genlight object sorted individuals by population names, indiviual name, for example to have a more informative gl.smearplot (showing banding patterns for populations). Also sorting by loci can be informative in some instances. This function provides the ability to sort individuals of a genlight object by providing the order of individuals or populations and also by loci metric providing the order of loci. See examples below for specifics.

Usage

gl.sort(x, sort.by = "pop", order.by = NULL, verbose = NULL)

Value

Returns a reordered genlight object. Sorts also the ind/loc.metrics and coordinates accordingly

Arguments

x

Genlight object containing SNP/silicodart genotypes [required].

sort.by

Either "ind", "pop" [default "pop"].

order.by

Vector used to order individuals or loci. Depending on the order.by parameter, this needs to be a vector of length of nPop(genlight) for populations or nInd(genlight) for individuals. If not specified alphabetical order of populations or individuals is used. For sort.by="ind" order.by can be also a vector specifying the order for each individual (for example another ind.metrics)

verbose

set verbosity

Author

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

Details

This is convenience function to facilitate sorting of individuals within the genlight object. For example if you want to visualise the "band" of population in a gl.smearplot then the order of individuals is important.

The parameter order.by needs to be a vector of length of nPop(genlight) for populations or nInd(genlight) for individuals. If not specified alphabetical order of populations or individuals is used. For sort.by="ind" order.by can be also a vector specifying the order for each individual (for example another ind.metrics).

See Also

Other data manipulation: gl.define.pop(), gl.drop.ind(), gl.drop.loc(), gl.drop.pop(), gl.edit.recode.pop(), gl.impute(), gl.join(), gl.keep.ind(), gl.keep.loc(), gl.keep.pop(), gl.make.recode.ind(), gl.merge.pop(), gl.reassign.pop(), gl.recode.ind(), gl.recode.pop(), gl.rename.pop(), gl.sample(), gl.sim.genotypes(), gl.subsample.ind(), gl.subsample.loc()

Examples

#sort by populations
bc <- gl.sort(bandicoot.gl)
#sort from West to East
bc2 <- gl.sort(bandicoot.gl, sort.by="pop" ,
order.by=c("WA", "SA", "VIC", "NSW", "QLD"))
#sort by missing values
miss <- rowSums(is.na(as.matrix(bandicoot.gl)))
bc3 <- gl.sort(bandicoot.gl, sort.by="ind", order.by=miss)
gl.smearplot(bc3)