Represents a cloud of points with colors
Description
The loadingplot
function represents positive values of a vector
and identifies the values above a given threshold. It can also
indicate groups of observations provided as a factor.
Such graphics can be used, for instance, to assess the weight of each variable (loadings) in a given analysis.
Usage
1 2 3 4 5 6 7 8 
Arguments
x 
either a vector with numeric values to be plotted, or a
matrixlike object containing numeric values. In such case, the

at 
an optional numeric vector giving the abscissa at which loadings are plotted. Useful when variates are SNPs with a known position in an alignement. 
threshold 
a threshold value above which values of x are identified. By default, this is the third quartile of x. 
axis 
an integer indicating the column of x to be plotted; used only if x is a matrixlike object. 
fac 
a factor defining groups of observations. 
byfac 
a logical stating whether loadings should be averaged by
groups of observations, as defined by 
lab 
a character vector giving the labels used to annotate values above the threshold; if NULL, names are taken from the object. 
cex.lab 
a numeric value indicating the size of annotations. 
cex.fac 
a numeric value indicating the size of annotations for groups of observations. 
lab.jitter 
a numeric value indicating the factor of randomisation for the position of annotations. Set to 0 (by default) implies no randomisation. 
main 
the main title of the figure. 
xlab 
the title of the x axis. 
ylab 
the title of the y axis. 
srt 
rotation of the labels; see ?text. 
adj 
adjustment of the labels; see ?text. 
... 
further arguments to be passed to the plot function. 
Value
Invisibly returns a list with the following components:
 threshold: the threshold used
 var.names: the names of observations above the threshold
 var.idx: the indices of observations above the threshold
 var.values: the values above the threshold
Author(s)
Thibaut Jombart t.jombart@imperial.ac.uk
Examples
1 2 3 4 5 6 7 8 9  x < runif(20)
names(x) < letters[1:20]
grp < factor(paste("group", rep(1:4,each=5)))
## basic plot
loadingplot(x)
## adding groups
loadingplot(x,fac=grp,main="My title",cex.lab=1)
