adegenet (version 1.2-3)

colorplot: 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(...)
## S3 method for class 'default':
colorplot(xy, X, axes=1:ncol(X), add.plot=FALSE, defaultLevel=0, ...)

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.

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.

...

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 the matched call.

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")

# a genetic example using a sPCA
if(require(spdep) & require(ade4)){
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 clinetP3 random tP4 local repulsion")
}