adegenet: colorplot – R documentation

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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(...)

## 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)

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