Plot an estimated baseline

Plots the baseline retained by preprocess or correct_baseline over the trace it was estimated from, annotated with the estimator, smoothing parameter and sampling interval that produced it.

Usage

plot_baseline(
  x,
  lambda = NULL,
  idx = 1,
  zoom = TRUE,
  col = "red",
  lty = 1,
  lwd = 2,
  add = FALSE,
  annotate = TRUE,
  ...
)

Arguments

x: A matrix or vector with an attached "estimated_baseline", or a list of such matrices, as returned by preprocess or correct_baseline with attach_baseline = TRUE.
lambda: Wavelength to plot, as a string or number. Optional for a single-wavelength chromatogram.
idx: Index or name of the chromatogram to plot, if x is a list. Defaults to 1.
zoom: Logical. Whether to scale the y axis to the baseline, letting the peaks run off the top of the panel. At full scale the baseline is usually pressed against the axis, which hides the estimate bending up into a peak. Defaults to TRUE; set FALSE to see the whole trace.
col, lty, lwd: Graphical parameters for the baseline itself. The trace beneath it is always drawn in gray.
add: Logical. Whether to draw the baseline over an existing plot rather than starting a new one, for comparing two estimates on the same trace. The title and annotation are drawn only by the first call, and ... is ignored. Defaults to FALSE.
annotate: Logical. Whether to annotate the plot with the estimator, its smoothing parameter and the sampling interval. Set FALSE when overlaying two estimates with add, since a single annotation cannot describe both; label them with legend instead. Defaults to TRUE.
...: Additional arguments to plot, which override the defaults chosen here — main = "" suppresses the title, and an explicit ylim overrides zoom.

Value

The annotation label, invisibly, so it can be reused in a legend. The plot is rendered to the active graphics device.

Details

The plot uses base graphics. For other plots, extract the baseline with get_baseline.

Author

Ethan Bass

Examples

# \donttest{
data(Sa)
x <- preprocess(Sa[1], dim1 = seq(10, 18, by = .01),
                dim2 = seq(200, 318, by = 2), attach_baseline = TRUE,
                show_progress = FALSE, cl = 1)
plot_baseline(x, lambda = 210)

# }