s-Plot of Spectra Data (Post PCA)

Source: R/sPlotSpectra.R

Produces a scatter plot of the correlation of the variables against their covariance for a chosen principal component. It allows visual identification of variables driving the separation and thus is a useful adjunct to traditional loading plots.

sPlotSpectra(spectra, pca, pc = 1, tol = 0.05, ...)

Arguments

spectra

An object of S3 class Spectra().

pca

The result of a pca calculation on Spectra (i.e. the output from c_pcaSpectra or r_pcaSpectra).

pc

An integer specifying the desired pc plot.

tol

A number describing the fraction of points to be labeled. tol = 1.0 labels all the points; tol = 0.05 labels approximately the most extreme 5 percent. Set to 'none' to completely suppress labels. Note that a simple approach based upon quantiles is used, assumes that both x and y are each normally distributed, and treats x and y separately. Thus, this is not a formal treatment of outliers, just a means of labeling points. Groups are lumped together for the computation.

...

Parameters to be passed to the plotting routines. Applies to base graphics only.

Value

The returned value depends on the graphics option selected (see GraphicsOptions()).

  • base: None. Side effect is a plot.

  • ggplot2: The plot is displayed, and a ggplot2 object is returned if the value is assigned. The plot can be modified in the usual ggplot2 manner.

References

Wiklund, Johansson, Sjostrom, Mellerowicz, Edlund, Shockcor, Gottfries, Moritz, and Trygg. "Visualization of GC/TOF-MS-Based Metabololomics Data for Identification of Biochemically Interesting Compounds Usings OPLS Class Models" Analytical Chemistry Vol.80 no.1 pgs. 115-122 (2008).

See also

Additional documentation at https://bryanhanson.github.io/ChemoSpec/

Author

Bryan A. Hanson (DePauw University), Tejasvi Gupta, Matthew J. Keinsley.

Examples


# This example assumes the graphics output is set to ggplot2 (see ?GraphicsOptions).
library("ggplot2")
data(SrE.IR)
pca <- c_pcaSpectra(SrE.IR)
myt <- expression(bolditalic(Serenoa) ~ bolditalic(repens) ~ bold(IR ~ Spectra))
p <- sPlotSpectra(spectra = SrE.IR, pca = pca, pc = 1, tol = 0.001)
p <- p + ggtitle(myt)
p