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Annotate peaks on a chromatogram

Source: R/plot_chroms.R
annotate_peaks.Rd

Adds text labels to peaks on a chromatogram plot produced by plot_chroms(). Peaks named in a peak table are labeled at their retention time, above the highest point of the chromatograms in idx between the peak's start and end. Peaks given as retention times are labeled at that time, above the highest plotted point within tol of it, and need no peak table; the label then marks the tallest trace in that window, whichever peak it belongs to.

Usage

annotate_peaks(
  p,
  loc,
  peak_table = NULL,
  chrom_list = NULL,
  label = NULL,
  lambda = NULL,
  idx = NULL,
  tol = 0.05,
  vjust = -0.5,
  ...
)

Arguments

p

A ggplot object produced by plot_chroms().

loc

Either a character vector of peak names from peak_table (e.g. c("V8", "V15")) or a numeric vector of retention times, in the units of the plot's time axis. If named, the names are used as labels.

peak_table

A peak_table object created by get_peaktable. Required when loc gives peak names.

chrom_list

A list of chromatograms in matrix format (timepoints × wavelengths). If no argument is provided here, the function will try to find the chrom_list object using the pointer in the peak_table.

label

Labels to display at each peak. Can be a character vector of labels (one per peak), or "rt" to use the retention times. If labels are not specified here, the names of loc will be applied, or if the loc vector is not named, the peak names will be used directly.

lambda

Wavelength(s) to use for locating the peak apex. Inherited from p if NULL (default). If multiple wavelengths are provided, the one with the highest absorbance at the peak's retention time is used.

idx

Index of chromatogram(s) to use for locating the peak apex. Inherited from p if NULL (default).

lambda and idx apply only to peak names; retention times use the plotted traces.

tol

Half-width of the window around each retention time in which the highest plotted point is found, in minutes. Defaults to 0.05. Ignored for peak names.

vjust

Vertical justification of the label relative to the peak apex. Defaults to -0.5.

...

Additional arguments passed to ggplot2::annotate().

Value

A ggplot object.

See also

plot_chroms(), plot_spectrum_inset()

Examples

if (requireNamespace("ggplot2", quietly = TRUE)) {
  data(Sa_warp)
  data(pk_tab)
  plot_chroms(Sa_warp, lambdas = 210, engine = "ggplot") |>
    annotate_peaks(c(C1="V7", C2="V9", C3="V15"), peak_table = pk_tab)
  plot_chroms(Sa_warp, lambdas = 210, engine = "ggplot") |>
    annotate_peaks(c(C1 = 12.18, C2 = 12.70))
}