Plot all spectra for chosen peak

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

Usage

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

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

Vector of chromatograms to plot.

engine

Which plotting engine to use: base, ggplot2, or plotly.

plot_spectrum

Logical. If TRUE, plots the spectrum of the chosen peak. Defaults to TRUE.

export_spectrum

Logical. If TRUE, invisibly returns the spectrum as a data.frame. Defaults to FALSE.

scale_spectrum

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

overlapping

Logical. If TRUE, plot spectra in single plot.

verbose

Logical. If TRUE, prints verbose output to console. Defaults to FALSE.

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.

peak

The name of a peak to plot (in character format).

...

Additional arguments to plot_spectrum.

Value

• If export_spectrum = FALSE (default), a plotly or ggplot object, or nothing if engine == "base".

• If export_spectrum = TRUE, invisibly returns a data.frame with wavelengths as rows and one column per sample encoding absorbance at each wavelength (normalized if scale_spectrum = TRUE).

Side effects

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

See also

Other visualization functions: boxplot.peak_table(), mirror_plot(), plot.peak_list(), plot.peak_table(), plot_chroms(), plot_chroms_heatmap(), plot_spectrum(), scan_chrom()

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)
}