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Plot all spectra for chosen peak.

Source: R/plot_spectrum.R
plot_all_spectra.Rd

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.

See also

plot_spectrum

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)
}