R: Represents a cloud of points with colors

loadingplot {adegenet} | R Documentation

## 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 t.jombart@imperial.ac.uk

### 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)

[Package adegenet version 2.1.4 Index]