A function to carry diagnostics on the PCA results for a
`Spectra`

object. Basically a wrapper to Filzmoser's
`pcaDiagplot`

which colors everything according to
the scheme stored in the `Spectra`

object. Works with PCA
results of either class `prcomp`

or class `princomp`

. Works
with either classical or robust PCA results.

```
pcaDiag(
spectra,
pca,
pcs = 3,
quantile = 0.975,
plot = c("OD", "SD"),
use.sym = FALSE,
...
)
```

- spectra
An object of S3 class

`Spectra`

.- pca
An object of class

`prcomp`

modified to include a character string (`$method`

) describing the pre-processing carried out and the type of PCA performed.- pcs
As per

`pcaDiagplot`

. The number of principal components to include.- quantile
As per

`pcaDiagplot`

. The significance criteria to use as a cutoff.- plot
A character string, indicating whether to plot the score distances or orthogonal distances, or both. Options are

`c("OD", "SD")`

.- use.sym
logical; if true, the color scheme is change to black and symbols are used for plotting.

- ...
Parameters to be passed to the plotting routines.

*Applies to base graphics only*.

The returned value depends on the graphics option selected (see `GraphicsOptions`

).

- base:
A data frame or list containing the data plotted. Assign the value and run

`str()`

or`names()`

on it to see what it contains. Side effect is a plot.- ggplot2:
The plot is displayed, and a

`ggplot2`

plot object is returned if the value is assigned. The plot can be modified in the usual`ggplot2`

manner. If you want the plotted values, you can access them via the base graphics mode.

If both plots are desired, the output should be directed to a file rather
than the screen. Otherwise, the 2nd plot overwrites the 1st in the active
graphics window. Alternatively, just call the function twice, once
specifying `OD`

and once specifying `SD`

.

K. Varmuza and P. Filzmoser *Introduction to Multivariate
Statistical Analysis in Chemometrics*, CRC Press, 2009.

`pcaDiagplot`

in package
`chemometrics`

for the underlying function. Additional documentation at
https://bryanhanson.github.io/ChemoSpec/

```
# This example assumes the graphics output is set to ggplot2 (see ?GraphicsOptions).
library("ggplot2")
data(SrE.IR)
pca <- c_pcaSpectra(SrE.IR, choice = "noscale")
p1 <- pcaDiag(SrE.IR, pca, pcs = 2, plot = "OD") + ggtitle("OD Plot")
p1
p2 <- pcaDiag(SrE.IR, pca, pcs = 2, plot = "SD") + ggtitle("SD Plot")
p2
```