Plot 2D spectra

nmrplot plots 2D spectra as contour plots, with contour levels set from the noise level.

using NMRTools
using CairoMakie   # static figures; use GLMakie for interactive

A single spectrum

spec2d = exampledata("2D_HN")
fig = nmrplot(spec2d)

Add 1D projections along either axis:

fig = nmrplot(exampledata("2D_HN"), xprojection=true, yprojection=true)

Plot a series of spectra in one call; colours cycle automatically and a legend can be added:

fig = nmrplot(exampledata("2D_HN_titration"), legend=:lt)

Contour colours and levels

Negative contours are shown by default as a faded version of the positive colour. Disable them or set a different colour:

fig = nmrplot(spec2d; negcontours=false)

fig = nmrplot(spec2d; negcolor=:red)

Pass levels as an integer to change the number of contour levels, or as a vector of absolute values to use explicit levels:

nmrplot(spec2d; levels=8)                    # 8 geometric levels from 5σ
nmrplot(spec2d; levels=[2e6, 4e6, 8e6])      # explicit positive levels

spacing sets the geometric ratio between levels (default 1.7):

nmrplot(spec2d; spacing=2.0, levels=10)

Keyboard navigation (GLMakie)

In GLMakie, press ↑ / ↓ to raise or lower all contour levels in the figure by one step (multiplied/divided by spacing). The key repeats while held. This works for any spectrum added with nmrplot or nmrplot!.

Pseudo-2D spectra

Pseudo-2D spectra (one frequency + one non-frequency dimension) support three display styles via the style keyword:

diffusiondata = exampledata("pseudo2D_XSTE")
diffusiondata = setgradientlist(diffusiondata, LinRange(0.02, 0.98, 10))
fig = nmrplot(diffusiondata, xlims=(7, 9.5))

┌ Warning: a maximum gradient strength of 0.55 T m⁻¹ is being assumed - this is roughly correct for modern Bruker systems but calibration is recommended
└ @ NMRTools.NMRBase ~/work/NMRTools.jl/NMRTools.jl/src/NMRBase/nmrdata.jl:315

fig = nmrplot(diffusiondata, xlims=(7, 9.5), style=:flat)

fig = nmrplot(diffusiondata, xlims=(7, 9.5), style=:waterfall)

Normalising a series

Pass a reference spectrum as normalize to put several spectra on the same contour levels, taking account of differences in scans and receiver gain:

spectra = exampledata("2D_HN_titration")
fig = nmrplot(spectra[[1, 11]]; normalize=spectra[1], title="first and last titration points")

3D spectra

Plot a plane or a strip of a 3D spectrum by selecting it first:

hnca = exampledata("3D_HNCA")
fig = nmrplot(hnca[:, Near(120.0), :]; title="¹H,¹³C plane at 120 ppm ¹⁵N")

Peaks

Overlay a peak list with nmrplot!(ax, peaks); see Peaks and peak lists.

Saving figures and layout

Saving and composing figures works as for 1D spectra; see Plot 1D spectra.

See Makie plot options for every keyword.