ChemoSpecUtils: plotScree – R documentation

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plotScree

Scree Plots from PCA or MIA Analysis of a Spectra or Spectra2D Object

Description

Functions that draw a traditional scree plot, or an alternative style that is perhaps more informative. These plots illustrate the variance explained by each component in a PCA or MIA analysis.

Usage

plotScree(pca, style = "alt", ...)

Arguments

pca

Either:

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.
An object of class mia produced by function miaSpectra2D.

style

Character. One of c("trad", "alt") giving the style of plot desired (traditional or alternative). "trad" is not supported for mia objects.

...

Additional parameters to be passed to plotting functions.

Value

None. Side effect is a plot.

Author(s)

Bryan A. Hanson, DePauw University.

References

The idea for the alternative style plot came from the NIR-Quimiometria blog by jrcuesta, at https://nir-quimiometria.blogspot.com/2012/02/pca-for-nir-spectrapart-004-projections.html

Examples

if (checkForPackageWithVersion("ChemoSpec", "5.1")) {
  library("ChemoSpec")
  data(metMUD1)

  pca <- c_pcaSpectra(metMUD1)
  plotScree(pca, style = "trad")
  plotScree(pca, style = "alt")
}

if (checkForPackageWithVersion("ChemoSpec2D", "0.3")) {
  library("ChemoSpec2D")
  data(MUD1)

  mia <- miaSpectra2D(MUD1)
  plotScree(mia, style = "alt")
}

ChemoSpecUtils

Functions Supporting Packages ChemoSpec and ChemoSpec2D

v0.4.96

GPL-3

Authors

Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>)

Initial release

2021-03-15