R: Plotting genlight objects

glPlot {adegenet} | R Documentation

## 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

### 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)

[Package adegenet version 2.1.4 Index]