plotLoadings {ChemoSpec}

Plot PCA Loadings for a Spectra Object

Description

Creates a multi-panel plot of loadings along with a reference spectrum.

Usage

plotLoadings(spectra, pca, loads = c(1), ref = 1, ...)

Arguments

spectra

An object of S3 class Spectra().

pca

An object of class prcomp, modified to include a list element called $method, a character string describing the pre-processing carried out and the type of PCA performed (it appears on the plot). This is automatically provided if ChemoSpec functions c_pcaSpectra or r_pcaSpectra were used to create pca.

loads

An integer vector giving the loadings to plot. More than 3 loadings creates a useless plot using the default graphics window.

ref

An integer specifying the reference spectrum to plot, which appears at the bottom of the plot.

...

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.

Author(s)

Bryan A. Hanson (DePauw University), Tejasvi Gupta.

See Also

c_pcaSpectra for an example. See plot2Loadings to plot two loadings against each other, and sPlotSpectra for an alternative approach. Additional documentation at https://bryanhanson.github.io/ChemoSpec/