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Plot spectrum from peak table

Source: R/plot_spectrum.R
plot_spectrum.Rd

Plots the trace and/or spectrum for a given peak or retention time in a peak_table object or a list of chromatograms.

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 at the given peak or retention time.

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.

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.

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'. Plots can be produced using either base R graphics, ggplot2, or plotly, according to the value of the engine argument.

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.

See also

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

Author

Ethan Bass

Examples

if (FALSE) { # interactive()
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)
}