plot.peak_list: Plot fitted peak shapes.

In ethanbass/chromatographR: Chromatographic Data Analysis Toolset

Plot fitted peak shapes.

Description

Visually assess integration accuracy by plotting fitted peaks over trace.

Usage

## S3 method for class 'peak_list'
plot(
  x,
  ...,
  chrom_list,
  idx = 1,
  lambda = NULL,
  points = FALSE,
  ticks = FALSE,
  a = 0.5,
  color = NULL,
  cex.points = 0.5,
  numbers = FALSE,
  cex.font = 0.5,
  y.offset = 25,
  plot_purity = FALSE,
  res,
  index = NULL
)

Arguments

x	A peak_list object. Output from the get_peaks function.
...	Additional arguments to main plot function.
chrom_list	List of chromatograms (retention time x wavelength matrices)
idx	Index or name of chromatogram to be plotted.
lambda	Wavelength for plotting.
points	Logical. If TRUE, plot peak maxima. Defaults to FALSE.
ticks	Logical. If TRUE, mark beginning and end of each peak. Defaults to FALSE.
a	Alpha parameter controlling the transparency of fitted shapes.
color	The color of the fitted shapes.
cex.points	Size of points. Defaults to 0.5
numbers	Whether to number peaks. Defaults to FALSE.
cex.font	Font size if peaks are numbered. Defaults to 0.5.
y.offset	Y offset for peak numbers. Defaults to 25.
plot_purity	Whether to add visualization of peak purity.
res	time resolution for peak fitting
index	This argument is deprecated. Please use idx instead.

Value

No return value, called for side effects.

Side effects

Plots a chromatographic trace from the specified chromatogram (chr) at the specified wavelength (lambda) with fitted peak shapes from the provided peak_list drawn underneath the curve.

Author(s)

Ethan Bass

See Also

get_peaks

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

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