glPlot: Plotting genlight objects

In adegenet: Exploratory Analysis of Genetic and Genomic Data

Plotting genlight objects

Description

genlight object can be plotted using the function glPlot, which is also used as the dedicated plot method. These functions relie on image to represent SNPs data. More specifically, colors are used to represent the number of second allele for each locus and individual.

Usage

glPlot(x, col=NULL, legend=TRUE, posi="bottomleft", bg=rgb(1,1,1,.5),...)

## S4 method for signature 'genlight'
plot(x, y=NULL, col=NULL, legend=TRUE, posi="bottomleft", bg=rgb(1,1,1,.5),...)

Arguments

x	a genlight object.
col	an optional color vector; the first value corresponds to 0 alleles, the last value corresponds to the ploidy level of the data. Therefore, the vector should have a length of (ploidy(x)+1).
legend	a logical indicating whether a legend should be added to the plot.
posi	a character string indicating where the legend should be positioned. Can be any concatenation of "bottom"/"top" and "left"/"right".
bg	a color used as a background for the legend; by default, transparent white is used; this may not be supported on some devices, and therefore background should be specified (e.g. bg="white").
...	further arguments to be passed to image.
y	ununsed argument, present for compatibility with the plot generic.

Author(s)

Thibaut Jombart [e-mail]

See Also

- genlight: class of object for storing massive binary SNP data.

- glSim: a simple simulator for genlight objects.

- glPca: PCA for genlight objects.

Examples

## Not run: 
## simulate data
x <- glSim(100, 1e3, n.snp.struc=100, ploid=2)

## default plot
glPlot(x)
plot(x) # identical plot

## disable legend
plot(x, leg=FALSE)

## use other colors
plot(x, col=heat.colors(3), bg="white")

## End(Not run)

adegenet documentation built on Feb. 16, 2023, 6 p.m.