Plot spectra by clicking on the chromatogram

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.

Usage

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

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 using the pointer in the peak_table.
idx: Numerical index of chromatogram you wish to plot, or "max" to automatically select the chromatogram with the highest signal intensity at the specified peak or retention time.
lambda: The wavelength used for plotting chromatographic traces and determining signal intensity.
plot_spectrum: Logical. If TRUE, plots the spectrum of the chosen peak. Defaults to TRUE.
peak_table: A peak_table object created by get_peaktable.
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, invisibly returns the spectrum as a data.frame. Defaults to FALSE.
...: Additional arguments to plot_spectrum.

Value

Invisibly returns the numeric index of the scan selected by the user.

Details

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.

Side effects

If engine == "base", plots are rendered to the active graphics device.

Author

Ethan Bass

Examples

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