adegenet: glPlot – R documentation

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glPlot

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 t.jombart@imperial.ac.uk

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

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release