loadingplot: Represents a cloud of points with colors

In thibautjombart/adegenet: Exploratory Analysis of Genetic and Genomic Data

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, ...)

## Default S3 method:
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

Author(s)

Thibaut Jombart [e-mail]

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)

thibautjombart/adegenet documentation built on Feb. 8, 2025, 12:09 a.m.