adegenet (version 2.0.0)

loadingplot: 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

loadingplot(x, ...)
## S3 method for class 'default':
loadingplot(x, at=NULL, threshold=quantile(x,0.75),
            axis=1, fac=NULL, byfac=FALSE,
            lab=NULL, cex.lab=0.7, cex.fac=1, lab.jitter=0,
            main="Loading plot", xlab="Variables", ylab="Loadings",
            srt = 0, adj = NULL, ...)

Arguments

x

either a vector with numeric values to be plotted, or a matrix-like object containing numeric values. In such case, the x[,axis] is used as vector of values to be plotted.

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 matrix-like object.

fac

a factor defining groups of observations.

byfac

a logical stating whether loadings should be averaged by groups of observations, as defined by fac.

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

Examples

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)