plotNMRspec: Create and Plot an NMR Spectrum

Description

This function simulates simple NMR spectra. Only 1st order coupling can be handled -- there is currently no capacity for doublet of doublets and other such peaks. The field strength of the "instrument" is taken into account.

Usage

plotNMRspec(peaks, x.range = c(12, 0), MHz = 300, ppHz = 1,
  nuclei = "1H", pkLabs = TRUE, lab.pos = NULL, plot = TRUE, ...)

Arguments

peaks

A data frame with the following columns: delta, mult (multiplicity), J, area, pw. Multiplicity should be given by a number, so use 2 for a doublet. J is in Hz (use 0 for singlets). pw is the peak width at half-height in Hz.

x.range

A numeric vector of length 2 giving the ppm range desired.

MHz

Integer. The operating frequency of the instrument, in MHz.

ppHz

Integer, but numeric works too! Points per Hz: The number of data points per Hz to use in calculating the spectrum (passed as argument dd to makeSpec). The default (1) works well for 1H NMR spectra. For 13C NMR spectra, where the peaks are very narrow, one may need to increase the data density so that enough points define the peaks (a value of 4 is a good starting point). See Details.

nuclei

Character. One of c("1H", "13C"). Controls the spacing of the tick marks and labeling of the peaks.

pkLabs

Logical. If TRUE, and nuclei = 1H, the integral is drawn next to the peak. If FALSE, no labels are drawn.

lab.pos

A vector of label positions as along as the number of rows in peaks (the number of peaks in the spectrum). A numeric vector where 2 = left and 4 = right. This adjusts the positions of the labels to be either left or right of the peak as a way to avoid overlaps. The order must correspond to the order in peaks.

plot

Logical: Shall a plot be made?

…

Other parameters to be passed downstream. These may affect the plot. You can also include noise = some number to add noise (passed through to makeSpec). In this case, warnings are raised from the plotting routines, but they can be ignored.

Value

Returns a data frame of the type produced by makeSpec. See there for details. x values are in Hz.

Details

Note that this function uses Hz internally so that the x.range, which is in ppm, is multiplied by Mhz before being sent to makeSpec, and once there, makeSpec will multiply it by ppHz. Thus the total data points used is floor(ppHz * Mhz * abs(diff(x.range))). This approach ensures that peaks are not distorted when changing x.range for the same peak.list.

Note that ppHz can be numeric as well, due to the use of floor. This can be useful: if you wanted your simulated NMR spectrum to be composed of exactly 16384 data points as real data might be, you can call the function with ppHz specified like ppHz = 2^14/(12*500) and it works!

Examples

Run this code

# NOT RUN {
### A simulated 1H NMR spectrum

peaks1 <- data.frame(
	delta = c(1.3, 3.75, 3.9, 10.2),
	mult = c(3, 4, 2, 1),
	J = c(14, 14, 14, 0),
	area = c(3, 2, 1, 1),
	pw = c(2, 2, 2, 10))

res <- plotNMRspec(peaks1, x.range = c(12, 0), MHz = 500,
	main = "500 MHz Simulated 1H NMR Spectrum")

### Compare to the same data at 200 MHz and plot together

par(mfrow = c(2,1))
res <- plotNMRspec(peaks1, x.range = c(12, 0), MHz = 500,
	main = "500 MHz Simulated 1H NMR Spectrum")
res <- plotNMRspec(peaks1, x.range = c(12, 0), MHz = 200,
	main = "200 MHz Simulated 1H NMR Spectrum")
par(mfrow = c(1,1))

### Zoom in to show off

par(mfrow = c(2,1))
res <- plotNMRspec(peaks1, x.range = c(4.5, 1), MHz = 500,
	main = "500 MHz Simulated 1H NMR Spectrum")
res <- plotNMRspec(peaks1, x.range = c(4.5, 1), MHz = 200,
	main = "200 MHz Simulated 1H NMR Spectrum")
par(mfrow = c(1,1))

### A simulated 13C NMR spectrum

# This is substantially slower due to the large
# chemical shift range

peaks2 <- data.frame(
	delta = c(160, 155, 145, 143, 135, 60, 32),
	mult = rep(1, 7),
	J = rep(1, 7),
	area = c(0.1, 0.3, 0.3, 1, 1, 0.5, 0.5),
	pw = rep(1, 7))

res <- plotNMRspec(peaks2, x.range = c(180, 0), MHz = 200,
	main = "200 MHz Simulated 13C NMR Spectrum", ppHz = 4,
	pkLabs = FALSE, nuclei = "13C")

# Try repeating the above with ppHz = 1; note the peaks heights are not quite right
# as there are not enough data points to define the peak properly.

# }