chromatographR (version 0.4.4)

scan_chrom: Scan spectrum

Description

Convenience function to call plot_spectrum with what = "click".

Usage

scan_chrom(
  chrom_list,
  lambda,
  chr,
  peak_table = NULL,
  scale_spectrum = FALSE,
  spectrum_labels = TRUE,
  export_spectrum = FALSE,
  ...
)

Value

If export_spectrum is TRUE, returns the spectrum as a data.frame with wavelengths as rows and a single column encoding the absorbance (or normalized absorbance, if scale_spectrum is TRUE) at each wavelength. Otherwise, there is no return value.

Arguments

chrom_list

A list of chromatograms in matrix form (timepoints x wavelengths).

lambda

The wavelength to plot the trace at.

chr

Numerical index of chromatogram you wish to plot.

peak_table

The peak table (output from get_peaktable function).

scale_spectrum

Logical. If TRUE, scales spectrum to unit height. Defaults to FALSE.

spectrum_labels

Logical. If TRUE, plots labels on maxima in spectral plot. Defaults to TRUE.

export_spectrum

Logical. If TRUE, exports spectrum to console. Defaults to FALSE.

...

Additional arguments.

Side effects

Plots a chromatographic trace from the specified chromatogram (chr), at the specified wavelength (lambda) with a dotted red line to indicate the user-selected retention time. The trace is a single column from the chromatographic matrix.

If plot_spectrum is TRUE, plots the spectrum for the specified chromatogram at the user-specified retention time. The spectrum is a single

Author

Ethan Bass

Examples

if (FALSE) { # interactive()
data(Sa_pr)
scan_chrom(Sa_pr, lambda="210", chr=2, export_spectrum=TRUE)
}