plot_spectrum: Plot spectrum from peak table
In chromatographR: Chromatographic Data Analysis Toolset

plot_spectrum

R Documentation

Plot spectrum from peak table

Description

Plots the trace and/or spectrum for a given peak in peak.table object, or plots the spectrum a particular retention time for a given chromatogram.

Usage

plot_spectrum(
  loc,
  peak_table,
  chrom_list,
  chr = "max",
  lambda = "max",
  plot_spectrum = TRUE,
  plot_trace = TRUE,
  spectrum_labels = TRUE,
  scale_spectrum = FALSE,
  export_spectrum = FALSE,
  verbose = TRUE,
  what = c("peak", "rt", "click"),
  ...
)

Arguments

`loc`	The name of the peak or retention time for which you wish to extract spectral data.
`peak_table`	The peak table (output from `get_peaktable` function).
`chrom_list`	A list of chromatograms in matrix form (timepoints x wavelengths).
`chr`	Numerical index of chromatogram you wish to plot, or "max" to automatically plot the chromatogram with the largest signal.
`lambda`	The wavelength you wish to plot the trace at if plot_trace == TRUE and/or the wavelength to be used for the determination of signal abundance.
`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, exports spectrum to console. Defaults to FALSE.
`verbose`	Logical. If TRUE, prints verbose output to console. Defaults to TRUE.
`what`	What to look for. Either "peak" to extract spectral information for a certain peak, "rt" to scan by retention time, or "click" to manually select retention time by clicking on the chromatogram. Defaults to "peak" mode.
`...`	Additional arguments.

Details

Can be used to confirm the identity of a peak or check that a particular column in the peak table represents a single compound. Retention times can also be selected by clicking on the plotted trace if what == 'click'.

Value

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

Side effects

If plot_trace is TRUE, plots the chromatographic trace of the specified chromatogram (chr), at the specified wavelength (lambda) with a dotted red line to indicate the retention time given by loc. The trace is a single column from the chromatographic matrix.

If plot_spectrum is TRUE, plots the spectrum for the specified chromatogram at the specified retention time. The spectrum is a single row from the chromatographic matrix.