chromatographR (version 0.4.4)

plot_all_spectra: Plot all spectra for chosen peak.

Description

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

Usage

plot_all_spectra(
  peak,
  peak_table,
  chrom_list,
  chrs = "all",
  plot_spectrum = TRUE,
  export_spectrum = TRUE,
  scale_spectrum = TRUE,
  overlapping = TRUE,
  verbose = FALSE,
  ...
)

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.

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 profile matrices, each of the same dimensions (timepoints x components).

chrs

Vector of chromatograms to plot.

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.

...

Additional arguments to plot_spectrum.

Side effects

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

Author

Ethan Bass

See Also

plot_spectrum

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)
}