PCA.plot: Principal Component Analysis plotting functions

In Thakkera/StatsDemo: Demo package for the EBI metabolomics courses in Hinxton

Description

Plotting functions for PCA: for scores, loadings, scores and loadings simultaneously (a biplot), and variances (a screeplot, where the log of the explained variance is plotted for each PC).

Usage

## S3 method for class 'PCA'
scoreplot(object, pc = c(1,2),
                        pcscores = scores(object),
                        show.names = FALSE, xlab, ylab, xlim, ylim,
                        ...)
## S3 method for class 'PCA'
loadingplot(object, pc = c(1,2),
                          pcloadings = loadings(object),
                          scalefactor = 1, add = FALSE,
                          show.names = FALSE, xlab, ylab, xlim, ylim,
                          col = "blue", min.length = .01, varnames = NULL,
                          ...)
screeplot(object, type = c("scree", "percentage"), npc, ...)
## S3 method for class 'PCA'
biplot(x, pc = c(1,2),
       pcscores = scores(object),
       pcloadings = loadings(object),
       show.names = c("none", "scores", "loadings", "both"),
       score.col = 1, loading.col = "blue",
       min.length = .01, varnames = NULL, ...)

Arguments

object, x	an object of class "PCA" (see below).
pc	which PCs to show.
pcscores	what scores to plot. If given, this makes the object argument superfluous; the pc argument may still be used to select columns from the given pcscores.
pcloadings	what loadings to plot. If given, this makes the object argument superfluous; the pc argument may still be used to select columns from the given pcloadings.
scalefactor	scaling factor for the loadings; used internally, when the loadingplot function is called from within biplot.PCA.
add	logical, whether to add to the existing plot (again, useful when loadingplot is called from within biplot.PCA).
show.names	show names rather than plotting symbols. For loadingplot and scoreplot a logical (default: FALSE), for biplot one of 'scores', 'loadings', 'both' or 'none' (default).
xlab, ylab, xlim, ylim, col, ...	additional graphical arguments (see par).
npc	how many PCs to show in the scree plot (starting from 1).
type	show a real screeplot (scree) or show the percentage of variance explained (percentage).
score.col, loading.col	colours of the scores and loadings in a biplot.
min.length	minimal length of loading vectors to be plotted by arrows. Vectors that are too short lead to warning messages, are not interesting, and only clutter the graphic.
varnames	alternative vector of variable names.

Details

Score plots and loading plots show the amount of explained variance at the axis labels, but only when PCA has been performed at mean-centered data.

References

R. Wehrens: "Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and Life Sciences". Springer, Heidelberg, 2011.

See Also

PCA

Examples

data(wines)
wines.PC <- PCA(scale(wines))
scoreplot(wines.PC)
loadingplot(wines.PC)
biplot(wines.PC)
screeplot(wines.PC)

Thakkera/StatsDemo documentation built on Oct. 31, 2019, 12:12 a.m.