Skip to contents

Plot Spectra

Source: R/plot.R
plot_spectra.Rd

Plot a set of deconvoluted spectra.

Usage

plot_spectra(
  obj,
  ...,
  foc_rgn = NULL,
  what = c("si", "sup", "supal"),
  sfy = 1e+06,
  cols = NULL,
  names = NULL,
  xlab = "Chemical Shift [ppm]",
  ylab = paste("Signal Intensity [au] /", sfy),
  mar = c(4.1, 4.1, 1.1, 0.1),
  lgd = list()
)

Arguments

obj

An object of type decons0, decons1 or decons2. For details see Metabodecon Classes.

...

Additional arguments passed to the conversion function.

foc_rgn

Numeric vector of length 2 specifying the focus region in ppm (e.g. c(3.55, 3.35)). If NULL (default), the full spectrum is shown.

what

Which signal to plot: "supal" (aligned superposition, default with fallback to "sup" then "si"), "sup" (superposition) or "si" (raw).

sfy

Scaling factor for the y-axis.

cols

Character vector of colors, one per spectrum. Defaults to rainbow(n).

names

Character vector of legend labels. Defaults to spectrum names.

xlab

Label for the x-axis.

ylab

Label for the y-axis.

mar

A numeric vector of length 4, which specifies the margins of the plot.

lgd

Logical or list. If TRUE, a legend is drawn at "topright" with cex = 0.8. If a list, its elements are passed to legend() to override position, size, etc. Set show = FALSE inside the list (or pass lgd = FALSE) to hide.

Value

A plot of the deconvoluted spectra.

See also

plot_spectrum() for a much more sophisticated plotting routine suitable for plotting a single spectrum.

Author

2024-2025 Tobias Schmidt: initial version.

Examples

obj <- deconvolute(sim[1:4], sfr = c(3.55, 3.35))
#> 2026-04-10 07:15:54.62 Starting deconvolution of 4 spectra using 1 worker
#> 2026-04-10 07:15:54.62 Starting deconvolution of sim_01 using R (legacy) backend
#> 2026-04-10 07:15:54.62 Removing water signal
#> 2026-04-10 07:15:54.62 Removing negative signals
#> 2026-04-10 07:15:54.62 Smoothing signals
#> 2026-04-10 07:15:54.63 Starting peak selection
#> 2026-04-10 07:15:54.63 Detected 314 peaks
#> 2026-04-10 07:15:54.63 Removing peaks with low scores
#> 2026-04-10 07:15:54.63 Removed 287 peaks
#> 2026-04-10 07:15:54.63 Initializing Lorentz curves
#> 2026-04-10 07:15:54.63 MSE at peak tiplet positions: 4.0838805770844048836921
#> 2026-04-10 07:15:54.63 Refining Lorentz Curves
#> 2026-04-10 07:15:54.63 MSE at peak tiplet positions: 0.1609359876216345797140
#> 2026-04-10 07:15:54.64 MSE at peak tiplet positions: 0.0228015051613790313556
#> 2026-04-10 07:15:54.64 MSE at peak tiplet positions: 0.0071638016610617799920
#> 2026-04-10 07:15:54.64 Formatting return object as decon2
#> 2026-04-10 07:15:54.64 Finished deconvolution of sim_01
#> 2026-04-10 07:15:54.64 Starting deconvolution of sim_02 using R (legacy) backend
#> 2026-04-10 07:15:54.64 Removing water signal
#> 2026-04-10 07:15:54.64 Removing negative signals
#> 2026-04-10 07:15:54.64 Smoothing signals
#> 2026-04-10 07:15:54.65 Starting peak selection
#> 2026-04-10 07:15:54.65 Detected 316 peaks
#> 2026-04-10 07:15:54.65 Removing peaks with low scores
#> 2026-04-10 07:15:54.65 Removed 286 peaks
#> 2026-04-10 07:15:54.65 Initializing Lorentz curves
#> 2026-04-10 07:15:54.65 MSE at peak tiplet positions: 3.8338943428876719465848
#> 2026-04-10 07:15:54.65 Refining Lorentz Curves
#> 2026-04-10 07:15:54.65 MSE at peak tiplet positions: 0.1289481941626757499630
#> 2026-04-10 07:15:54.68 MSE at peak tiplet positions: 0.0135651899090413786964
#> 2026-04-10 07:15:54.68 MSE at peak tiplet positions: 0.0025556755331531087749
#> 2026-04-10 07:15:54.68 Formatting return object as decon2
#> 2026-04-10 07:15:54.68 Finished deconvolution of sim_02
#> 2026-04-10 07:15:54.68 Starting deconvolution of sim_03 using R (legacy) backend
#> 2026-04-10 07:15:54.68 Removing water signal
#> 2026-04-10 07:15:54.68 Removing negative signals
#> 2026-04-10 07:15:54.68 Smoothing signals
#> 2026-04-10 07:15:54.69 Starting peak selection
#> 2026-04-10 07:15:54.69 Detected 333 peaks
#> 2026-04-10 07:15:54.69 Removing peaks with low scores
#> 2026-04-10 07:15:54.69 Removed 308 peaks
#> 2026-04-10 07:15:54.69 Initializing Lorentz curves
#> 2026-04-10 07:15:54.69 MSE at peak tiplet positions: 1.4917065120183623516681
#> 2026-04-10 07:15:54.69 Refining Lorentz Curves
#> 2026-04-10 07:15:54.69 MSE at peak tiplet positions: 0.0569971157280155932279
#> 2026-04-10 07:15:54.70 MSE at peak tiplet positions: 0.0065629979536274852397
#> 2026-04-10 07:15:54.70 MSE at peak tiplet positions: 0.0013913916281140725414
#> 2026-04-10 07:15:54.70 Formatting return object as decon2
#> 2026-04-10 07:15:54.70 Finished deconvolution of sim_03
#> 2026-04-10 07:15:54.70 Starting deconvolution of sim_04 using R (legacy) backend
#> 2026-04-10 07:15:54.70 Removing water signal
#> 2026-04-10 07:15:54.70 Removing negative signals
#> 2026-04-10 07:15:54.70 Smoothing signals
#> 2026-04-10 07:15:54.71 Starting peak selection
#> 2026-04-10 07:15:54.71 Detected 325 peaks
#> 2026-04-10 07:15:54.71 Removing peaks with low scores
#> 2026-04-10 07:15:54.71 Removed 299 peaks
#> 2026-04-10 07:15:54.71 Initializing Lorentz curves
#> 2026-04-10 07:15:54.71 MSE at peak tiplet positions: 2.2382155282476525748336
#> 2026-04-10 07:15:54.71 Refining Lorentz Curves
#> 2026-04-10 07:15:54.71 MSE at peak tiplet positions: 0.0843491698981613247099
#> 2026-04-10 07:15:54.71 MSE at peak tiplet positions: 0.0101688144550079444944
#> 2026-04-10 07:15:54.71 MSE at peak tiplet positions: 0.0031861616084395915326
#> 2026-04-10 07:15:54.72 Formatting return object as decon2
#> 2026-04-10 07:15:54.72 Finished deconvolution of sim_04
#> 2026-04-10 07:15:54.72 Finished deconvolution of 4 spectra in 0.095 secs
plot_spectra(obj)