Description Usage Arguments Value Author(s) Examples
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.
1 2 3 4 
xy 
a numeric matrix with two columns (e.g. a matrix of spatial coordinates. 
X 
a matrixlike 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 
... 
further arguments to be passed to other methods. In

Invisibly returns a vector of colours used in the plot.
Thibaut Jombart t.jombart@imperial.ac.uk
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17  # 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("P1P2 in cline\tP3 random \tP4 local repulsion")
}
## End(Not run)

Loading required package: ade4
/// adegenet 2.0.1 is loaded ////////////
> overview: '?adegenet'
> tutorials/doc/questions: 'adegenetWeb()'
> bug reports/feature requests: adegenetIssues()
Loading required package: spdep
Loading required package: sp
Loading required package: Matrix
Attaching package: 'spdep'
The following object is masked from 'package:ade4':
mstree
PLEASE NOTE: The components "delsgs" and "summary" of the
object returned by deldir() are now DATA FRAMES rather than
matrices (as they were prior to release 0.018).
See help("deldir").
PLEASE NOTE: The process that deldir() uses for determining
duplicated points has changed from that used in version
0.09 of this package (and previously). See help("deldir").
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