Plot all spectra for chosen peak.

Plot multiple for a given peak in peak table. Wrapper for plot_spectrum.

Usage

plot_all_spectra(
  peak,
  peak_table,
  chrom_list,
  idx = "all",
  chrs = NULL,
  engine = c("base", "ggplot2", "plotly"),
  plot_spectrum = TRUE,
  export_spectrum = TRUE,
  scale_spectrum = TRUE,
  overlapping = TRUE,
  verbose = FALSE,
  what = c("peak", "rt", "idx"),
  ...
)

Arguments

peak: The name of a peak to plot (in character format).
peak_table: The peak table (output from get_peaktable function).
chrom_list: A list of chromatograms in matrix format (timepoints x components). If no argument is provided here, the function will try to find the chrom_list object used to create the provided peak_table.
idx: Vector of chromatograms to plot.
chrs: Deprecated. Please use idx instead.
engine: Which plotting engine to use: base, ggplot2, or plotly.
plot_spectrum: Logical. If TRUE, plots the spectrum of the chosen peak.
export_spectrum: Logical. If TRUE, exports spectrum to console. Defaults to FALSE.
scale_spectrum: Logical. If TRUE, scales spectrum to unit height.
overlapping: Logical. If TRUE, plot spectra in single plot.
verbose: Logical. If TRUE, 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, or idx to scan by numeric index. Defaults to "peak" mode.
...: Additional arguments to plot_spectrum.

Value

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

Side effects

If plot_spectrum is TRUE, plots the spectra for the specified chromatogram (idx) of the given peak. The spectrum is a single row from the chromatographic matrix.

Author

Ethan Bass

Examples

if (FALSE) { # interactive()
data(Sa_warp)
pks <- get_peaks(Sa_warp, lambda = "220")
pk_tab <- get_peaktable(pks)
plot_all_spectra(peak = "V13", peak_table = pk_tab, overlapping = TRUE)
}