Overlay fitted peak shapes on chromatograms

Draws fitted peak shapes over chromatographic traces to assess integration accuracy.

Usage

# S3 method for class 'peak_list'
plot(
  x,
  ...,
  chrom_list,
  idx = 1,
  lambda = NULL,
  targets = NULL,
  tol = 0.1,
  pad = 0.5,
  points = FALSE,
  ticks = FALSE,
  alpha = 0.5,
  color = NULL,
  cex.points = 0.5,
  numbers = FALSE,
  cex.font = 0.5,
  digits = 2,
  y.offset = 0.03,
  plot_purity = c("none", "ratio", "curves", "curves_local"),
  purity_args = list(),
  res
)

Arguments

x: A peak_list object. Output from the get_peaks function.
...: Additional arguments to main plot function. The plot is titled with the sample, wavelength and peak model by default; pass main to change the title, or main = "" to omit it, and xaxt = "n" or yaxt = "n" to hide an axis.
chrom_list: List of chromatograms (retention time × 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. Defaults to the first wavelength in x.
targets: Optional target retention times, as a numeric vector or a table of targets (see targeted_analysis). If supplied, the plot is zoomed to the span of every peak whose apex falls within tol of a target, or, for a target with no such peak, whose boundaries (widened by tol) enclose it. The vertical axis is rescaled to the contents of that window, so that small peaks are not flattened against the axis. Defaults to NULL.
tol: Numeric. Half-width of the window around each target, in minutes, regardless of the time unit of chrom_list. Either a single value applied to every target, or a vector giving a separate tolerance for each target. A tol column in targets takes precedence. Defaults to 0.1. Ignored if targets is NULL.
pad: Fraction of the selected peak span to add on either side when zooming. Defaults to 0.5, which keeps neighboring peaks in view. An explicit xlim or ylim passed through ... takes precedence over the zoom; if xlim is given, the vertical axis is rescaled to that window instead.
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, the color depends on the fitted model type.
cex.points: Size of points. Defaults to 0.5.
numbers: Labels drawn above each peak. TRUE labels peaks with their index in the peak list, and "rt" labels them with their retention time, which can be passed back to targets. Defaults to FALSE.
cex.font: Font size if peaks are numbered. Defaults to 0.5.
digits: Number of decimal places for retention time labels when numbers = "rt". Defaults to 2.
y.offset: Vertical offset of peak numbers, as a fraction of the height of the plot region. Defaults to 0.03.
plot_purity: Whether and how to draw peak purity traces below the chromatogram. "none" (default) draws nothing. "ratio" plots the purity ratio as lollipops on a log scale from 0.01 to 100, clamping values beyond it: blue for pure (ratio < 1), red for impure, with a dotted reference line at ratio = 1. "curves" draws spectral dissimilarity (1 - r^2) against the noise threshold on a fixed [0, 1] scale. The threshold is a gray dotted line, and the dissimilarity line is blue where it falls below the threshold (pure) and red where it exceeds it (impure). "curves_local" is the same, but rescales each peak to its own maximum. TRUE maps to "curves" and FALSE to "none".
purity_args: A named list of additional arguments controlling the purity calculation, e.g. list(background_correction = "none"). See get_purity. Arguments that do not apply to the per-peak purity trace drawn here (metric, min_run and try) are ignored, so the same list can be passed to get_peaks and to this function.
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 must contain columns rt, height, start, end, and sd, with additional columns depending on the fit type.

Width parameters are rescaled using the time units of x.

A peak whose shape cannot be drawn is skipped with a warning.

Side effects

Plots the trace of chromatogram idx at wavelength lambda, with the fitted peak shapes from x filled in beneath it.

Author

Ethan Bass

Examples

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

plot(pks, targets = 11.12, ticks = TRUE)

op <- par(mfrow = c(1, 2))
for (t in c(12.19, 14.41)) plot(pks, targets = t)

par(op)