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Makie plotting

NMRTools provides a Makie extension with nmrplot and nmrplot! for interactive or publication-quality figures while preserving NMR plotting conventions (reversed chemical-shift axes, sensible defaults for 1D/2D/3D).

To activate the extension, load NMRTools and a Makie backend (for example CairoMakie or GLMakie):

using NMRTools
using CairoMakie

Quick start

1D spectrum

fig = nmrplot(exampledata("1D_1H"))
 Downloading artifact: 1D_1H

Set the plot range with the xlims option - the spectrum will rescale vertically to match:

fig = nmrplot(exampledata("1D_1H"), xlims=(-1, 4.5))

Use the mutating form to overlay additional spectra onto the same axis:

nmrplot!(fig, exampledata("1D_1H") / 2)

2D spectrum

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

Add 1D projections along each axis:

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

Plot a series of 2Ds in one call:

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

Or add spectra one-by-one with nmrplot! and then add a legend in standard Makie style:

dats = exampledata("2D_HN_titration")
fig, ax = nmrplot(dats[1], title="", xlims=(-120, -128))
nmrplot!(fig, dats[5])
nmrplot!(fig, dats[10])
axislegend(ax)

When plotting a small number of 2Ds, Makie's default cycle is used instead of a rainbow gradient:

fig = nmrplot(exampledata("2D_HN_titration")[[1, 5, 10]])

Contours are drawn at positive and negative levels by default. You can control colours and disable negative contours:

fig = nmrplot(spec2d; negcontours=false)

or adjust negative contour colours:

fig = nmrplot(spec2d; negcolor=:red)

Pseudo-2D spectra (one frequency + one non-frequency dimension)

Choose a style with the style keyword:

  • style=:heatmap (default)
  • style=:flat (overlaid 1D slices)
  • style=:waterfall (3D slice view)

Example pseudo-2D diffusion plot:

diffusiondata = exampledata("pseudo2D_XSTE")
# set the gradient strengths - which varied from 2% to 98% of the max, over 10 points
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:306

The default is a heatmap, and flat/waterfall styles are also available:

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

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

Plot placement and layout

nmrplot works directly with Makie layouts and can be composed with other Makie plots:

fig = Figure()

nmrplot(fig[1, 1], exampledata("1D_1H"); title="", xlims=(-1, 4.5))
nmrplot(fig[1, 2], exampledata("2D_HN"); title="", xlims=(6, 10))
scatter(fig[2,:], randn(100))