Example code for "Further examples"

[songtaogui]

Thanks for this wonderful pkg,

I would like to use GeneticsMakie to draw some gwas results similar to those in the "Patterns of association and LD" example in the README.md:

However, I have no idea how to start after reading the doc.

Could you please provide the example code for this example?

Thanks a lot!

All the best,

SongtaoGui

[mmkim1210]

Hey @songtaogui,

The key is to use GeneticsMakie.plotld! function which does not have a separate documentation page at the moment.

Here is an example code:

using GeneticsMakie, CairoMakie, Statistics

begin
    @info "Set up example parameters"
    chr, range1, range2 = "2", 1500, 4000
    ntraits = 3
    nsnps = 600
    traits = ["Example 1", "Example 2", "Example 3"]
    geno = rand(nsnps, 5)
    ld = cor(geno, dims = 2)
    ld = ld.^2
    textstart = 325
    textend = 375
    x = range(0.5, 9.5, length = nsnps)
    y = range(0.5, ntraits - 0.5, length = ntraits)
    p = rand(nsnps, ntraits)
    signs = rand([-1, 1], nsnps, ntraits)
    signedp = p .* signs
end

begin
    @info "Plot example figure"
    f = Figure(resolution = (306, 750))
    axs = [Axis(f[i, 1]) for i in 1:2]
    @info "Plot first axis"
    colormax = ceil(max(abs.(extrema(p))...))
    heatmap!(axs[1], x, y, signedp, colorrange = (-colormax, colormax), colormap = :RdBu_11)
    axs[1].yticks = (y, reverse(traits))
    axs[1].yticklabelsize = 6
    axs[1].yticklabelpad = 3
    hidexdecorations!(axs[1])
    hideydecorations!(axs[1], ticklabels = false)
    hidespines!(axs[1], :r, :l, :b)
    axs[1].spinewidth = 0.5
    rowsize!(f.layout, 1, 6 * (ntraits + 1))
    lines!(axs[1], fill(x[textstart], 2), [0, 3], color = :black, linewidth = 1.0)
    lines!(axs[1], fill(x[textend], 2), [0, 3], color = :black, linewidth = 1.0)
    text!(axs[1], "start", position = (x[textstart], last(y) + step(y) / 2), align = (:center, :bottom), fontsize = 5)
    text!(axs[1], "end", position = (x[textend], last(y) + step(y) / 2), align = (:center, :bottom), fontsize = 5)
    ylims!(axs[1], 0, 4)
    GeneticsMakie.labelgenome(f[1, 1, Top()], chr, range1, range2)
    @info "Plot second axis"
    GeneticsMakie.plotld!(axs[2], ld, color = "black")
    rowsize!(f.layout, 2, Aspect(1, 0.5))
    hidespines!(axs[2])
    ylims!(axs[2], 0, 5)
    rowgap!(f.layout, 0)
    resize_to_layout!(f)
    save("example.png", f, px_per_unit = 4)
end

And the following is the generated output: