ChemoSpec (version 5.0.88)

plotScree: 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.

Value

None. Side effect is a plot.

Functions

• plotScree: Traditional scree plot

• plotScree2: Alternate scree plot

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.

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

# NOT RUN {
data(metMUD1)
pca <- c_pcaSpectra(metMUD1)
plotScree(pca, main = "metMUD1 NMR Data")
plotScree2(pca, main = "metMUD1 NMR Data")

# }