Plot spectra by clicking on the chromatogram

Usage

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

Arguments

chrom_list: A list of chromatograms in matrix format (timepoints x wavelengths). If no argument is provided here, the function will try to find the chrom_list object used to create the provided peak_table.
idx: Numerical index of chromatogram you wish to plot.
lambda: The wavelength to plot the trace at.
plot_spectrum: Logical. Whether to plot the spectrum or not.
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.
chr: Deprecated. Please use idx instead.
...: Additional arguments.

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.

Side effects

Plots a chromatographic trace from the specified chromatogram (idx), 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 row from the chromatographic matrix.

Author

Ethan Bass

Examples

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