plotScree {ChemoSpecUtils}

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.

...

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.

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", 6.0)) {
  library("ChemoSpec")
  data(metMUD1)

  pca <- c_pcaSpectra(metMUD1)
  p1 <- plotScree(pca, style = "trad")
  p1
  p2 <- plotScree(pca, style = "alt")
  p2
}

if (checkForPackageWithVersion("ChemoSpec2D", 0.5)) {
  library("ChemoSpec2D")
  data(MUD1)

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