Plot spectrum from peak table

Visualizes chromatographic traces and/or UV spectra for a selected peak, retention time, or scan index from a peak_table or list of chromatograms. Spectra can also be exported as a data.frame when export_spectrum = TRUE.

Usage

plot_spectrum(
  loc = NULL,
  peak_table,
  chrom_list = NULL,
  idx = "max",
  lambda = "max",
  plot_spectrum = TRUE,
  plot_trace = TRUE,
  spectrum_labels = TRUE,
  scale_spectrum = FALSE,
  export_spectrum = FALSE,
  verbose = TRUE,
  what = c("peak", "rt", "idx", "click"),
  engine = c("base", "plotly", "ggplot2"),
  ...
)

Arguments

loc: The peak, retention time, or scan index from which to extract spectral data.
peak_table: A peak_table object created by get_peaktable.
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.
plot_trace: Logical. If TRUE, plots the trace of the chosen peak at lambda. Defaults to TRUE.
spectrum_labels: Logical. If TRUE, plots labels on maxima in spectral plot. Defaults to TRUE.
scale_spectrum: Logical. If TRUE, scales spectrum to unit height. Defaults to FALSE.
export_spectrum: Logical. If TRUE, invisibly returns the spectrum as a data.frame. Defaults to FALSE.
verbose: Logical. If TRUE (default), prints verbose output to console.
what: What to look for. Either peak to extract spectral information for a certain peak, rt to scan by retention time, idx to scan by numeric index, or click to manually select retention time by clicking on the chromatogram. Defaults to "peak" mode.
engine: Which plotting engine to use: base, ggplot2, or plotly.
...: Additional arguments.

Value

If export_spectrum = FALSE (default), returns a plotly or ggplot object according to the specified engine. No value is returned when engine = "base".
If export_spectrum is TRUE, invisibly returns the spectrum as a data.frame with wavelengths as rows and a single column encoding the absorbance (normalized, if scale_spectrum = TRUE).

Details

This function can be used to confirm the identity of a peak or assess whether a peak table column likely represents a single compound. Retention times may also be selected interactively by clicking on a chromatographic trace when what = "click".

When plot_trace is TRUE, the chromatographic trace for the specified chromatogram (idx) is plotted at wavelength lambda, with a dotted red line indicating the selected retention time (loc). The trace corresponds to a single column of the chromatographic matrix.

When plot_spectrum is TRUE, the UV spectrum at the specified retention time is plotted. The spectrum corresponds to a single row of 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)
pks <- get_peaks(Sa, lambda = "220.00000")
pk_tab <- get_peaktable(pks)
oldpar <- par(no.readonly = TRUE)
par(mfrow = c(2, 1))
plot_spectrum(loc = "V10", peak_table = pk_tab, what = "peak")
par(oldpar)
}