R: Scree Plots of PCA Results for a Spectra Object

plotScree {ChemoSpec} | R Documentation

## Scree Plots of PCA Results for a Spectra Object

### Description

Functions to draw a traditional scree plot or an alternative that is perhaps more useful. These illustrate the importance of the components in a PCA analysis.

### Usage

    plotScree(pca, ...)

    plotScree2(pca, ...)

### Arguments

`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`.
`...` | Additional parameters to be passed to plotting functions.

### Details

If you add `$method` to the PCA results from other packages, this will plot a scree plot for any PCA results, not just those from `Spectra` objects.

### Value

None. Side effect is a plot.

### Functions

- `plotScree`: Traditional scree plot

- `plotScree2`: Alternate scree 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

https://github.com/bryanhanson/ChemoSpec

### Examples

    data(metMUD1)
    pca <- c_pcaSpectra(metMUD1)
    plotScree(pca, main = "metMUD1 NMR Data")
    plotScree2(pca, main = "metMUD1 NMR Data")

[Package ChemoSpec version 4.4.97 Index]