# Simplex heatmap **URL:** \ **Category:** Visualization\ **Tags:** gmt\ **Created:** [July 1, 2022, 7:53pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640 "2022-07-01T19:53:13Z")\ **Posts on this page:** 16\ **Page:** 1
**Author:** ![bryce](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/bryce/32/15193_2.png) [@bryce](https://discourse.julialang.org/u/bryce)\ **Post date:** [July 1, 2022, 7:53pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/1 "2022-07-01T19:53:13Z")
I’m trying to generate a heatmap to visualize the output of a function evaluated on a grid of points over the unit 2-simplex. Here’s an example of the sort of data I’m working with: ```julia using Plots, Combinatorics, StatsBase function simplex_grid(num_outcomes, points_per_dim) num_points = multinomial(num_outcomes-1, points_per_dim) points = Array{Float64,2}(undef, num_outcomes, num_points) for (p,comb) in enumerate(with_replacement_combinations(1:num_outcomes, points_per_dim)) distr = counts(comb, 1:num_outcomes) ./ points_per_dim points[:,p] = distr end return points end function bary2cart(points) x = (2 .* points[3,:] .+ points[1,:]) ./ dropdims(sum(points, dims=1), dims=1) ./ 2 y = √3 / 2 .* points[1,:] ./ dropdims(sum(points, dims=1), dims=1); return (x,y) end points_per_dim = 30 num_outcomes = 3 grid = simplex_grid(num_outcomes, points_per_dim) (x,y) = bary2cart(grid) z = rand(length(x)) ``` The best solutions I’ve come up with so far are 1) a scatter plot with hexagonal markers: ```julia plot(showaxis=false, grid=false, ticks=false, xlims=(-.08,1.08), ylims=(-.08,.√.75+.08)) scatter!(x,y, zcolor=z, markerstrokewidth=0, markershape=:hexagon, markersize=8, label="") plot!([0,.5,1,0],[0,√.75,0,0], color=:black, markeralpha=0, label="") annotate!(.5, √.75+.07, text("A", 12)) annotate!(-.05, -.05, text("B", 12)) annotate!(1.05,-.05, text("C", 12)) ``` ![hexagons](https://global.discourse-cdn.com/julialang/original/3X/3/e/3e5ac365896a5d790c0d0f4d0f13fa4421a794cf.png) or 2) a surface with the camera directly above: ```julia plot(showaxis=false, grid=false, ticks=false, xlims=(-.08,1.08), ylims=(-.08,.√.75+.08)) surface!(x,y,z, zcolor=z, camera=(0,90)) plot!([0,.5,1,0],[0,√.75,0,0], color=:black, markeralpha=0, label="") ``` ![surface](https://global.discourse-cdn.com/julialang/original/3X/d/d/dd47012e1c37f0847942e99a0490754bf6de2272.png) But both of these have significant drawbacks. The hexagons tend to have gaps or overlaps, and don’t allow any interpolation. The surface doesn’t allow annotations, and has weirdly jagged edges. Any suggestions for how to improve on (or replace) either of these would be appreciated! Related but less important: I also tried plotting the barycentric coordinates directly, but couldn’t figure out how to get the view aligned orthogonal to the plane of the simplex. Is there anywhere I can find a basic explanation of how the “camera” keyword works? ---
**Author:** ![juliohm](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/juliohm/32/215266_2.png) [@juliohm](https://discourse.julialang.org/u/juliohm)\ **Post date:** [July 1, 2022, 8:09pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/2 "2022-07-01T20:09:51Z")
Are you after a ternary plot? > [@Ternary plots](https://discourse.julialang.org/t/ternary-plots/60867): > > I am looking to replicate the figure below (from Wikipedia on the Dirichlet distribution). Is there any way to do this currently in Julia (the vertical color scale is not that important)? [Dirichlet] There are open issues in plotting packages to support these maps. I know that TernaryPlots.jl had something working at some point: > **[GitHub - jacobusmmsmit/TernaryPlots.jl: Ternary/simplex plotting recipe/addon...](https://github.com/jacobusmmsmit/TernaryPlots.jl)** > > Ternary/simplex plotting recipe/addon for Plots.jl - GitHub - jacobusmmsmit/TernaryPlots.jl: Ternary/simplex plotting recipe/addon for Plots.jl Also, Zulip has a discussion with various more advanced tricks: [https://julialang.zulipchat.com/#narrow/stream/225542-helpdesk/topic/Can.20a.20recipe.20be.20used.20for.20ternary.20plots.3F](https://julialang.zulipchat.com/#narrow/stream/225542-helpdesk/topic/Can.20a.20recipe.20be.20used.20for.20ternary.20plots.3F) ---
**Author:** ![joa-quim](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/joa-quim/32/227_2.png) [@joa-quim](https://discourse.julialang.org/u/joa-quim)\ **Post date:** [July 1, 2022, 10:04pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/3 "2022-07-01T22:04:36Z")
Examples of ternary plots [Ternary plots](https://www.generic-mapping-tools.org/GMTjl_doc/examples/ternary/) with GMT.jl ---
**Author:** ![bryce](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/bryce/32/15193_2.png) [@bryce](https://discourse.julialang.org/u/bryce)\ **Post date:** [July 6, 2022, 5:22pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/4 "2022-07-06T17:22:28Z")
I had looked into TernaryPlots.jl, but heatmaps are listed under “work in progress”. ---
**Author:** ![juliohm](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/juliohm/32/215266_2.png) [@juliohm](https://discourse.julialang.org/u/juliohm)\ **Post date:** [July 6, 2022, 5:29pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/5 "2022-07-06T17:29:07Z")
What about the thread in Zulip? Maybe there is a heatmap there? It is been a while I read it… ---
**Author:** ![bryce](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/bryce/32/15193_2.png) [@bryce](https://discourse.julialang.org/u/bryce)\ **Post date:** [July 6, 2022, 5:42pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/6 "2022-07-06T17:42:24Z")
GMT seems powerful, but its Julia interface seems _very_ poorly documented. I’ve managed to get the following figure, but I can’t figure out how to annotate it. I’d like to add lots of labels, starting with something like the A/B/C annotations from the example above. Any suggestions? ![GMT](https://global.discourse-cdn.com/julialang/original/3X/4/8/485a830534138cc0e87f8d3609a4c942100f2bf3.png) ```julia using GMT grid = simplex_grid(num_outcomes, points_per_dim) m = Matrix{Float64}(undef,496,4) m[:,1:3] .= grid' m[:,4] = generate_data(grid) C = makecpt(T=(0,maximum(m[:,4])*1.001)) ternary(m, show=true, marker=:p, image=true, cmap=C, markersize=.01, region=(0,1,0,1,0,1), frame=(grid=0.1, ticks=0.1, annot=0.5)) ``` If possible, I’d also like to add annotations using LatexStrings, such as: ```julia using LatexStrings annotate!(0.5, -.05, text(L"\left< 0, \frac{1}{2}, \frac{1}{2}\right>", 12)) ``` but since that doesn’t seem to work right in any of the plotting libraries I wouldn’t be surprised if it were just totally infeasible. ---
**Author:** ![rafael.guerra](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/rafael.guerra/32/216610_2.png) [@rafael.guerra](https://discourse.julialang.org/u/rafael.guerra)\ **Post date:** [July 6, 2022, 8:35pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/7 "2022-07-06T20:35:15Z")
> [@bryce](#): > > add annotations using LatexStrings, such as …, but since that doesn’t seem to work right in any of the plotting libraries Fyi, it seems to work well with Plots.jl’s `pgfplotsx()` backend: ![Plots_pgfplotsx_heatmap_annotate_LaTeXStrings](https://global.discourse-cdn.com/julialang/original/3X/8/9/89000acae04c37e4347760afcc8294250ede8fb6.png) ```julia using LaTeXStrings, Plots; pgfplotsx() heatmap(rand(10,10)); annotate!(5.5, 5.5, text(L"\left< 0, \frac{1}{2}, \frac{1}{2}\right>", 16)) ``` ---
**Author:** ![joa-quim](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/joa-quim/32/227_2.png) [@joa-quim](https://discourse.julialang.org/u/joa-quim)\ **Post date:** [July 6, 2022, 9:46pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/8 "2022-07-06T21:46:48Z")
> [@bryce](#): > > GMT seems powerful, but its Julia interface seems _very_ poorly documented. I know that the documentation is lagging behind but no need to exaggerate also. Doesn’t the link that I posted above show numerous examples on how to add … `A/B/C` labeling and other examples? (posting it again) [https://www.generic-mapping-tools.org/GMTjl\_doc/examples/ternary/ternary\_examples/](https://www.generic-mapping-tools.org/GMTjl_doc/examples/ternary/ternary_examples/) All that respect frames is described in the [manual](https://www.generic-mapping-tools.org/GMTjl_doc/documentation/common_opts/common_opts/) … and we can’t say it’s a short description. Regarding LaTex, that’s a different issue. Yes, it should be possible. [GMT does it](https://docs.generic-mapping-tools.org/dev/cookbook/gmt-latex.html?highlight=latex) but depends on a full LaTex installation, which something that doesn’t really pleases me. But so far it seems the only option. Put the latex string in a `label="@[\nabla^4 \psi - \Delta \sigma_{xx}^2@[ (MPa)"` like in the GMT example I linked to. Never tried but no reason it should not work … as long as the GMT conditions are met. And ```julia help?> ternary ``` gives also _some_ info ---
**Author:** ![bryce](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/bryce/32/15193_2.png) [@bryce](https://discourse.julialang.org/u/bryce)\ **Post date:** [July 7, 2022, 3:53pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/9 "2022-07-07T15:53:36Z")
I appreciate your help, and I don’t want to get into an argument over tone on the internet, but please understand that it’s incredibly frustrating to be told to RTFM when you’ve already been trying to understand that manual for many hours. There’s certainly tons of information in the general GMT manual, but it’s quite challenging to parse if you don’t already know the ins and outs of GMT. Specifically, it’s very hard to figure out how things will translate to the Julia interface and it’s very hard to track down the right search terms for features one doesn’t already know. Here’s my current status: ```julia ternary(m, show=true, image=true, region=(0,1,0,1,0,1), frame=(grid=0, ticks=0.5, annot=0), vertex_labels="3/1/2", labels=(["0, .5, .5"],[".5, 0, .5"],[".5, .5, 0"])) ``` ![GMT](https://global.discourse-cdn.com/julialang/original/3X/7/e/7ea5bc87f115a91d17b03d0c98e587d317f0bf32.png) There are lots of things I’d like to add, but the most pressing is to make it clear that the labels like [0, .5, .5] refer to the point on the edge of the simplex. I could imagine several ways of doing this, but haven’t managed to get any of them working. One option might be various GMT config options. It _seems_ like this line should make the ticks larger (and if it worked, there’d be a number of other interesting config options I’d like to explore), but it doesn’t appear to change anything: ```julia gmtset(MAP_TICK_LENGTH=2) ``` Or if I could overlay a scatter plot on top of the heatmap, I could do something like this to emphasize those points: ```julia ternary([0 0.5 0.5; 0.5 0 0.5; 0.5 0.5 0], frame=(grid=0, ticks=0, annot=0), noclip=true, marker=:p, markersize=.2, show=true) ``` ![midpoints](https://global.discourse-cdn.com/julialang/original/3X/6/8/68c32c69e71d7ff672f50c0b6d577485dd099aff.png) But what seems to me like the obvious way to do this in Julia (calling ternary!) doesn’t work, and my searching hasn’t turned up any alternatives. Many of the other things I’d like to do could be managed if I had a way to add arbitrary text to an arbitrary location in the figure, but again, I can’t find the right GMT command to do that. Any tips would be wonderful; thanks again! ---
**Author:** ![joa-quim](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/joa-quim/32/227_2.png) [@joa-quim](https://discourse.julialang.org/u/joa-quim)\ **Post date:** [July 7, 2022, 4:36pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/10 "2022-07-07T16:36:26Z")
Sorry for your doc-frustation. I share it because I try to keep adding layers of it and seem to be failing. The `gmtset(MAP_TICK_LENGTH=2,)` should work, but note the trailing comma needed because it’s a named tuple, but looks it’s not. I will have to look at that. But you can obtain a similar effect (not exactly equal because the `gmtset` form is supposed to be permanent until the figure is generated) with the `par=( put-your-settings-here )` alternative. Regarding plotting a scatter plot on an image. Isn’t what that example does? Or you want a different image? ```julia ternary("@ternary.txt", marker=:p, image=true, clockwise=true, frame=(annot=:auto, grid=:a, ticks=:a, alabel="Clay", blabel="Silt", clabel="Sand", suffix=" %"), par=(MAP_TICK_LENGTH=2,), show=true) ``` ![GMTjl_tmp-fs8](https://global.discourse-cdn.com/julialang/original/3X/b/6/b6ac30dce3bf7e2a69e82b620667552c697dd893.png) ---
**Author:** ![joa-quim](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/joa-quim/32/227_2.png) [@joa-quim](https://discourse.julialang.org/u/joa-quim)\ **Post date:** [July 7, 2022, 4:47pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/11 "2022-07-07T16:47:57Z")
I can obtain the same figure as above by splitting it into two commands. This means you can get an image with one dataset and do a scatter plot with another. ```julia ternary("@ternary.txt", image=true, clockwise=true, frame=(annot=:auto, grid=:a, ticks=:a, alabel="Clay", blabel="Silt", clabel="Sand", suffix=" %"), par=(MAP_TICK_LENGTH=2,)) ternary!("@ternary.txt", marker=:p, show=true) ``` ---
**Author:** ![bryce](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/bryce/32/15193_2.png) [@bryce](https://discourse.julialang.org/u/bryce)\ **Post date:** [July 7, 2022, 8:27pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/12 "2022-07-07T20:27:53Z")
I had show=true in both commands 🤦, and the result was an uninformative error message. ---
**Author:** ![joa-quim](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/joa-quim/32/227_2.png) [@joa-quim](https://discourse.julialang.org/u/joa-quim)\ **Post date:** [July 7, 2022, 11:16pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/13 "2022-07-07T23:16:49Z")
Nothing I can do to improve that error message. The **!** form tells to append to a figure. If that figure was not initialized with a call to a method without the **!** form the resulting postscript file is invalid and the error you saw is issued by ghostscript, not GMT. ---
**Author:** ![joa-quim](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/joa-quim/32/227_2.png) [@joa-quim](https://discourse.julialang.org/u/joa-quim)\ **Post date:** [July 8, 2022, 4:12pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/14 "2022-07-08T16:12:48Z")
@bryce, [ternary](https://www.generic-mapping-tools.org/GMTjl_doc/documentation/modules/ternary/index.html#ternary) man page. Feel free to propose improvements to the parts that made you suffer more. ---
**Author:** ![bryce](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/bryce/32/15193_2.png) [@bryce](https://discourse.julialang.org/u/bryce)\ **Post date:** [July 8, 2022, 11:47pm UTC](https://discourse.julialang.org/t/simplex-heatmap/83640/15 "2022-07-08T23:47:32Z")
Thanks, I’ll take a look and see if I have any suggestions. On a related note, when I try to add another series to the plot with ternary!, I’m sometimes getting the following error: ```julia psbasemap [ERROR]: Bad interval in -B option (x-component, a-info): (null) gave interval = 0 psbasemap [ERROR]: Bad interval in -B option (y-component, a-info): (null) gave interval = 0 psbasemap [ERROR]: Option -B parsing failure. Correct syntax: -B[p|s][x|y|z][+a|n|p][+l|L