plot.peak_table: Plot spectrum from peak table
In chromatographR: Chromatographic Data Analysis Toolset

plot.peak_table

R Documentation

Plot spectrum from peak table

Description

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,
  what = "peak",
  chr = "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
)

Arguments

`x`	The peak table (output from `get_peaktable` function).
`...`	Additional arguments.
`loc`	The name of the peak or retention time that you wish to plot.
`chrom_list`	A list of chromatograms in matrix form (timepoints x wavelengths).
`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`.
`chr`	Numerical index of chromatogram you wish to plot; "max" to plot the chromatogram with the largest signal; or "all" to plot spectra for all chromatograms.
`lambda`	The wavelength you wish to plot the trace at (if `plot_chrom` is 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.
`box_plot`	Logical. If TRUE, plots box plot using categories defined by `vars`.
`vars`	Independent variables for boxplot.
`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.

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. Can also be used to create simple box-plots to examine the distribution of a peak with respect to variables defined in sample metadata.

Value

If export_spectrum is TRUE, returns the spectrum as a data.frame with wavelengths as rows and columns encoding the absorbance (or normalized absorbance, if scale_spectrum is TRUE) for the specified sample(s). 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.

If box_plot is TRUE, produces a boxplot from the specified peak with groups provided by vars.