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Plot a chromatogram or chromatograms with an inset UV spectrum

Source: R/plot_spectrum.R
plot_spectrum_inset.Rd

Plots a chromatogram (either a single trace or multiple traces) with an inset UV spectrum for a specified peak. Dotted lines connect the peak apex to the corners of the inset box.

Usage

plot_spectrum_inset(
  loc,
  peak_table,
  chrom_list = NULL,
  idx = "max",
  lambda = "max",
  position = "topright",
  inset_width = 0.35,
  inset_height = 0.35,
  ylim = NULL,
  xlim = NULL,
  engine = "ggplot",
  scale_spectrum = TRUE,
  verbose = getOption("verbose"),
  inset_text_size = 8,
  ...
)

Arguments

loc

Peak name or vector of names in the peak table (e.g. "V10").

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.

idx

Index of chromatogram(s) to plot. If "max" (default) or a scalar, plots a single trace using plot_spectrum(). If a vector, plots multiple traces using plot_chroms().

lambda

Wavelength to use for the chromatographic trace and for locating the peak apex. Either a numeric value or "max" (default) to use the wavelength of maximum absorbance.

position

Position of the inset. One of "topright" (default), "topleft", "top", "left", or "right". Alternatively, a numeric vector of length 2 giving the proportional coordinates of the bottom-left corner, e.g., c(0.6, 0.6), used together with inset_width and inset_height.

inset_width

Width of the inset as a proportion of the plot width. Defaults to 0.35.

inset_height

Height of the inset as a proportion of the plot height. Defaults to 0.35.

ylim

Y axis limits for the main plot. Passed to plot_chroms() or plot_spectrum().

xlim

X axis limits for the main plot. Passed to plot_chroms() or plot_spectrum().

engine

Plotting engine. Currently only "ggplot" is supported.

scale_spectrum

Logical. If TRUE, scales spectrum to unit height. Defaults to FALSE.

verbose

Logical. If TRUE (default), prints verbose output to console.

inset_text_size

Base size for text elements in inset. Defaults to 8.

...

Additional arguments passed to plot_chroms() or plot_spectrum().

Value

A ggplot object.

See also

plot_spectrum(), plot_chroms()

Examples

if (requireNamespace("ggplot2", quietly = TRUE)) {
  data(pk_tab)
  data(Sa_warp)
  # single trace with inset spectrum
  plot_spectrum_inset("V15", peak_table = pk_tab)

  # multiple traces, inset in the center
  plot_spectrum_inset("V15", peak_table = pk_tab, idx=c(1:4),
  position = "top")

  # manual inset placement
  plot_spectrum_inset("V15", peak_table = pk_tab,
                      position = c(0.6, 0.3),
                      inset_width = 0.35, inset_height = 0.25)

  # multiple peaks with a list of positions
  plot_spectrum_inset(c("V15", "V26"), peak_table = pk_tab,
                      position = list(c(0.3, 0.5), c(0.65, 0.3)),
                      inset_width = 0.3, inset_height = 0.3)#'
                      }