Annotate peaks on a chromatogram

Adds text labels to peaks on a chromatogram plot produced by plot_chroms(). Peak retention times and intensities are looked up automatically from the peak table.

Usage

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

Arguments

p

A ggplot object produced by plot_chroms().

loc

A character vector of peak names (e.g. c("V8", "V15")). If named, the names are used as labels (e.g. c(Sinigrin = "V8", 1ME = "V15")).

peak_table

A peak_table object created by get_peaktable.

chrom_list

A list of chromatograms in matrix format (timepoints x 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), "rt" to use retention times from the peak table. 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 is used.

idx

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

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="V9", C2="V11", C3="V17"), peak_table = pk_tab)
}