Plot spectrum from peak table

Plots the trace and/or spectrum for a given peak in peak table.

Usage

# S3 method for class 'peak_table'
plot(
  x,
  loc,
  chrom_list = NULL,
  what = "peak",
  idx = "max",
  lambda = "max",
  plot_spectrum = TRUE,
  plot_trace = TRUE,
  box_plot = FALSE,
  vars = NULL,
  spectrum_labels = TRUE,
  scale_spectrum = FALSE,
  export_spectrum = FALSE,
  verbose = TRUE,
  engine = c("base", "plotly", "ggplot"),
  ...
)

Arguments

x: The peak table (output from get_peaktable).
loc: A vector specifying the peak(s) or retention time(s) to plot. If missing when what = "peak", you are prompted for a peak name. When a value is returned (see below), only the first element of loc is used, with a warning.
chrom_list: A list of chromatograms in matrix format (timepoints × wavelengths). If no argument is provided here, the function will try to find the chrom_list object using the pointer in the peak_table.
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. "click" requires engine = "base".
idx: Numerical index of chromatogram you wish to plot; "max" (default) to plot the chromatogram with the largest value for the peak in the peak table; or "all" to plot spectra for all chromatograms.
lambda: The wavelength at which to plot the trace. "max" (default) selects the wavelength at which the spectrum at loc is highest.
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.
box_plot: Logical. If TRUE, plots box plot using categories defined by vars.
vars: Character vector of column names in the sample metadata, used as the right-hand side of the boxplot formula.
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, invisibly returns the spectrum as a data.frame. Defaults to FALSE.
verbose: Logical. If TRUE (default), prints the index and name of each chromatogram plotted, with its retention time, wavelength and absorbance.
engine: Plotting backend to use. One of "base", "ggplot", or "plotly". "ggplot2" is also accepted here, for backward compatibility, but "ggplot" is the spelling the other plotting functions take.
...: Additional arguments to boxplot.

Value

If export_spectrum = FALSE (default), a plotly or ggplot object, or nothing if engine == "base".
If export_spectrum = TRUE, the spectrum as a data.frame with wavelengths as rows and one column per sample giving absorbance at each wavelength (normalized if scale_spectrum = TRUE).

Details

Use it to confirm the identity of a peak, or to check that a particular column in the peak table represents a single compound. It also draws simple box plots of the distribution of a peak against variables defined in sample metadata.

When plot_trace is TRUE, plots the trace of chromatogram idx at wavelength lambda, with a dotted red line at the retention time given by loc. When plot_spectrum is TRUE, plots the spectrum of the same chromatogram at that retention time. When box_plot is TRUE, draws a boxplot of the peak with groups defined by vars.

Side effects

If engine == "base", plots are rendered to the active graphics device.

Author

Ethan Bass