R: Represents a cloud of points with colors

colorplot {adegenet} | R Documentation

## Represents a cloud of points with colors

### Description

The `colorplot` function represents a cloud of points with colors corresponding to a combination of 1,2 or 3 quantitative variables, assigned to RGB (Red, Green, Blue) channels. For instance, this can be useful to represent up to 3 principal components in space. Note that the property of such representation to convey multidimensional information has not been investigated.

`colorplot` is a S3 generic function. Methods are defined for particular objects, like `spca` objects.

### Usage

    colorplot(...)

    ## Default S3 method:
    colorplot(xy, X, axes=NULL, add.plot=FALSE, defaultLevel=0, transp=FALSE, alpha=.5, ...)

### Arguments

`xy` | a numeric matrix with two columns (e.g. a matrix of spatial coordinates.
`X` | a matrix-like containing numeric values that are translated into the RGB system. Variables are considered to be in columns.
`axes` | the index of the columns of X to be represented. Up to three axes can be chosen. If null, up to the first three columns of X are used.
`add.plot` | a logical stating whether the colorplot should be added to the existing plot (defaults to FALSE).
`defaultLevel` | a numeric value between 0 and 1, giving the default level in a color for which values are not specified. Used whenever less than three axes are specified.
`transp` | a logical stating whether the produced colors should be transparent (TRUE) or not (FALSE, default).
`alpha` | the alpha level for transparency, between 0 (fully transparent) and 1 (not transparent); see `?rgb` for more details.
`...` | further arguments to be passed to other methods. In `colorplot.default`, these arguments are passed to plot/points functions. See `?plot.default` and `?points`.

### Value

Invisibly returns a vector of colours used in the plot.

### Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

### Examples

    # a toy example
    xy <- expand.grid(1:10,1:10)
    df <- data.frame(x=1:100, y=100:1, z=runif(100,0,100))
    colorplot(xy,df,cex=10,main="colorplot: toy example")

    ## Not run:
    # a genetic example using a sPCA
    if(require(spdep)){
    data(spcaIllus)
    dat3 <- spcaIllus$dat3
    spca3 <- spca(dat3,xy=dat3$other$xy,ask=FALSE,type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1)
    colorplot(spca3, cex=4, main="colorplot: a sPCA example")
    text(spca3$xy[,1], spca3$xy[,2], dat3$pop)
    mtext("P1-P2 in cline\tP3 random \tP4 local repulsion")
    }

    ## End(Not run)

[Package adegenet version 2.1.4 Index]