SpecHelpers (version 0.2.7)

plot2DNMRspec: Draw a 2D NMR Spectrum

Description

This function simulates 2D 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

plot2DNMRspec(peaks, x.range = c(0, 12), MHz = 300, ppHz = 1,
  type = "COSY", M = NULL, levels = seq(0.5, 1, by = 0.1), ...)

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. Must be increasing.

MHz

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

ppHz

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. 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 ppHz * Mhz * abs(diff(x.range)). This approach ensures that peaks are not distorted when changing x.range for the same peak.list.

type

The type of 2D spectrum desired. One of c("COSY", "TOCSY").

M

An adjacency matrix indicating which peaks are coupled. The order of rows and columns must be the same as in peaks.

levels

A vector of levels for the contour plot. Must be in (0...1).

…

Parameters to be passed to the plotting function.

Value

Returns a matrix.

See Also

makeSpec

Examples

# NOT RUN {
### ethyl 2-ethyl-3-oxobutyrate
### Set up data

peaks1 <- data.frame(
#             A     B     C     D     E     F
	delta = c(4.20, 3.34, 2.23, 1.88, 1.28, 0.94),
	mult = c(4, 3, 1, 5, 3, 3),
	J = c(14, 14, 0, 14, 14, 14),
	area = c(2, 1, 3, 2, 3, 3),
	pw = c(2, 2, 2, 2, 2, 2))

#              A, B, C, D, E, F
AM <- matrix(c(0, 0, 0, 0, 1, 0,  # A
               0, 0, 0, 1, 0, 0,  # B
               0, 0, 0, 0, 0, 0,  # C
               0, 1, 0, 0, 0, 1,  # D
               1, 0, 0, 0, 0, 0,  # E
               0, 0, 0, 1, 0, 0), # F
			   ncol = 6)

### 1D 1H NMR plot for reference
# CRAN checks will skip some examples to save time


jnk <- plotNMRspec(peaks = peaks1, x.range = c(0, 5), MHz = 500,
main = "1H NMR of ethyl 2-ethyl-3-oxobutyrate")

### 2D COSY plot

res <- plot2DNMRspec(peaks = peaks1, x.range = c(0, 5), MHz = 500, ppHz = 1, M = AM,
main = "COSY of ethyl 2-ethyl-3-oxobutyrate")

### 2D TOCSY plot

# }
# NOT RUN {
res <- plot2DNMRspec(peaks = peaks1, x.range = c(0, 5), MHz = 500, ppHz = 1,
levels = c(0.85, 0.9, 0.95), type = "TOCSY",
main = "TOCSY of ethyl 2-ethyl-3-oxobutyrate")
# }