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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 two nearest 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 × 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, and the inset shows its spectrum. If a vector, plots one trace per chromatogram, and the inset overlays their spectra.

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. When loc names several peaks, a list with one position per peak.

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().

xlim

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

engine

Plotting engine. Currently only "ggplot" is supported.

scale_spectrum

Logical. If TRUE (the default), scales the inset spectrum to unit height.

verbose

Logical. If TRUE, prints the index and name of each chromatogram plotted, with its retention time, wavelength and absorbance. Defaults to getOption("verbose").

inset_text_size

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

...

Additional arguments passed to plot_chroms().

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("V13", peak_table = pk_tab)

  # multiple traces, inset in the center
  plot_spectrum_inset("V13", peak_table = pk_tab, idx=c(1:4),
  position = "top")

  # manual inset placement
  plot_spectrum_inset("V13", 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("V13", "V25"), peak_table = pk_tab,
                      position = list(c(0.3, 0.5), c(0.65, 0.3)),
                      inset_width = 0.3, inset_height = 0.3)
                      }