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Overlay fitted peak shapes on chromatograms

Source: R/plot.peak_list.R
plot.peak_list.Rd

Visually assess peak integration accuracy by overlaying fitted peak shapes over chromatographic traces.

Usage

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

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). If missing, extracted from environment using the pointer in x.

idx

Index or name of chromatogram to plot from chrom_list.

lambda

Wavelength (column) to use for plotting.

points

Logical. If TRUE, display peak apex locations as points. Defaults to FALSE.

ticks

Logical. If TRUE, mark peak boundaries with tick marks. Defaults to FALSE.

alpha

Transparency of fitted peak shapes. Defaults to 0.5.

color

Color used to fill fitted peak shapes. If NULL, a default color is chosen based on the fitted model type.

cex.points

Size of points. Defaults to 0.5.

numbers

If TRUE, label peaks with numeric identifiers. 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

Logical. If TRUE, overlays peak purity traces based on peak boundaries. Defaults to FALSE.

res

Time resolution for peak fitting. If missing, inferred from chrom_list.

Value

No return value, called for side effects.

Details

The appearance of fitted peaks depends on the "fit" attribute of x, which may be "gaussian", "egh", "bemg", or "raw".

Peak lists are expected to contain columns such as rt, height, start, end, and sd, with additional parameters depending on the fit type.

Time units in x are used to rescale width parameters for plotting.

Peak rendering errors are silently ignored.

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.

See also

get_peaks

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

Author

Ethan Bass

Examples

data(Sa_warp)
pks <- get_peaks(chrom_list = Sa_warp[1], lambdas = 210)
plot(pks, points = TRUE, ticks = TRUE)