plot_spectrum: Plot spectrum from peak table

In ethanbass/chromatographR: Chromatographic Data Analysis Toolset

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 = NULL,
  peak_table,
  chrom_list,
  idx = "max",
  lambda = "max",
  plot_spectrum = TRUE,
  plot_trace = TRUE,
  spectrum_labels = TRUE,
  scale_spectrum = FALSE,
  export_spectrum = FALSE,
  verbose = TRUE,
  what = c("peak", "rt", "idx", "click"),
  engine = c("base", "plotly", "ggplot2"),
  chr = NULL,
  ...
)

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).
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 used to create the provided peak_table.
idx	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, idx to scan by numeric index, or click to manually select retention time by clicking on the chromatogram. Defaults to "peak" mode.
engine	Which plotting engine to use: base, ggplot2, or plotly.
chr	Deprecated. Please use idx instead.
...	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. If export_spectrum is FALSE, the output depends on the plotting engine. If engine == "plotly", returns a plotly object containing the specified plots. Otherwise, if engine == "base", there is no return value.

Side effects

• If plot_trace is TRUE, plots the chromatographic trace of the specified chromatogram (idx), 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.

Author(s)

Ethan Bass

See Also

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

Examples

data(Sa)
pks <- get_peaks(Sa, lambda = "220.00000")
pk_tab <- get_peaktable(pks)
oldpar <- par(no.readonly = TRUE)
par(mfrow = c(2, 1))
plot_spectrum(loc = "V10", peak_table = pk_tab, what = "peak")
par(oldpar)

ethanbass/chromatographR documentation built on April 17, 2025, 10:55 a.m.