Apply the transform_func on positions, to work in nonlinear scale (#14)

* Apply the transform_func as well in order to work in nonlinear scale * Fix typos * Transform back until we have `space == :transformed` * Add an example of the Julia microbenchmarks in beeswarm * scale -> scales.md * dict not dataframe in example * Finally fix example * Even more unconventional example * fix Octave * Fix color type * Better file structure for examples * clean up * Do not edit marker position if group is empty This fixes issues encountered when using missing or NaN data.
MakieOrg · Apr 20, 2024 · a0e233b · a0e233b
1 parent d4c1056
commit a0e233b
Show file tree

Hide file tree

Showing 8 changed files with 240 additions and 7 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,4 +6,4 @@
 */node_modules/*
 .DS_Store
 
-docs/src/examples.md
+docs/src/examples/examples.md
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,10 +1,14 @@
 [deps]
 AlgebraOfGraphics = "cbdf2221-f076-402e-a563-3d30da359d67"
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterVitepress = "4710194d-e776-4893-9690-8d956a29c365"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 PalmerPenguins = "8b842266-38fa-440a-9b57-31493939ab85"
 RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b"
+Rsvg = "c4c386cf-5103-5370-be45-f3a111cca3b8"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 SwarmMakie = "0b1c068e-6a84-4e66-8136-5c95cafa83ed"
diff --git a/docs/make.jl b/docs/make.jl
@@ -65,7 +65,7 @@ withenv("JULIA_DEBUG" => "Literate") do # allow Literate debug output to escape
 end
 
 # As a special case, literatify the examples.jl file in docs/src to Documenter markdown
-Literate.markdown(joinpath(@__DIR__, "src", "examples.jl"), joinpath(@__DIR__, "src"); flavor = Literate.DocumenterFlavor(), postprocess = _replace_example_with_figure)
+Literate.markdown(joinpath(@__DIR__, "src", "examples", "examples.jl"), joinpath(@__DIR__, "src", "examples"); flavor = Literate.DocumenterFlavor(), postprocess = _replace_example_with_figure)
 
 makedocs(;
     modules=[SwarmMakie],
@@ -80,7 +80,11 @@ makedocs(;
         "Introduction" => "introduction.md",
         "Algorithms" => "algorithms.md",
         "Gutters" => "gutters.md",
-        "Examples" => "examples.md",
+        "Examples" => [
+            "examples/examples.md",
+            "Nonlinear scales" => "examples/scales.md",
+            "Unconventional use" => "examples/unconventional.md"
+        ],
         "API Reference" => "api.md",
         "Source code" => literate_pages,
     ],

diff --git a/docs/src/examples.jl → docs/src/examples/examples.jl b/docs/src/examples.jl → docs/src/examples/examples.jl
diff --git a/docs/src/examples/scales.md b/docs/src/examples/scales.md
@@ -0,0 +1,3 @@
+# Scaled beeswarm plots
+
+Beeswarm plots can also be plotted in log-scale axes!
diff --git a/docs/src/examples/unconventional.md b/docs/src/examples/unconventional.md
@@ -0,0 +1,212 @@
+# Unconventional swarm plots
+
+You can use swarm plots to simply separate scatter markers which share the same `x` coordinate, and distinguish them by color and marker type.
+
+
+## The Julia benchmark plot
+
+```@example julia-benchmark
+# Load the required Julia packages
+using Base.MathConstants
+using CSV
+using DataFrames
+using AlgebraOfGraphics, SwarmMakie, CairoMakie
+using StatsBase, CategoricalArrays
+
+# Load benchmark data from file
+benchmarks =
+    CSV.read(download("https://raw.githubusercontent.com/JuliaLang/Microbenchmarks/master/bin/benchmarks.csv"), DataFrame; header = ["language", "benchmark", "time"])
+
+# Capitalize and decorate language names from datafile
+dict = Dict(
+    "c" => "C",
+    "julia" => "Julia",
+    "lua" => "LuaJIT",
+    "fortran" => "Fortran",
+    "java" => "Java",
+    "javascript" => "JavaScript",
+    "matlab" => "Matlab",
+    "mathematica" => "Mathematica",
+    "python" => "Python",
+    "octave" => "Octave",
+    "r" => "R",
+    "rust" => "Rust",
+    "go" => "Go",
+);
+benchmarks[!, :language] = [dict[lang] for lang in benchmarks[!, :language]]
+
+# Normalize benchmark times by C times
+ctime = benchmarks[benchmarks[!, :language] .== "C", :]
+benchmarks = innerjoin(benchmarks, ctime, on = :benchmark, makeunique = true)
+select!(benchmarks, Not(:language_1))
+rename!(benchmarks, :time_1 => :ctime)
+benchmarks[!, :normtime] = benchmarks[!, :time] ./ benchmarks[!, :ctime];
+
+# Compute the geometric mean for each language
+langs = [];
+means = [];
+priorities = [];
+for lang in benchmarks[!, :language]
+    data = benchmarks[benchmarks[!, :language] .== lang, :]
+    gmean = geomean(data[!, :normtime])
+    push!(langs, lang)
+    push!(means, gmean)
+    if (lang == "C")
+        push!(priorities, 1)
+    elseif (lang == "Julia")
+        push!(priorities, 2)
+    else
+        push!(priorities, 3)
+    end
+end
+
+# Add the geometric means back into the benchmarks dataframe
+langmean = Dict(langs .=> tuple.(means, priorities))
+benchmarks.geomean = first.(getindex.((langmean,), benchmarks.language))
+benchmarks.priority = last.(getindex.((langmean,), benchmarks.language))
+
+# Put C first, Julia second, and sort the rest by geometric mean
+sort!(benchmarks, [:priority, :geomean]);
+
+langs = CategoricalArray(benchmarks.language)
+bms = CategoricalArray(benchmarks.benchmark)
+
+f, a, p = beeswarm(
+    langs.refs, benchmarks.normtime;
+    color = bms.refs,
+    colormap = :Set2_8,
+    # markersize = 5,
+    marker = Circle,
+    axis = (;
+        yscale = log10,
+        xticklabelrotation = 0, 
+        xticklabelsize = 12,
+        xticksvisible = false,
+        topspinecolor = :gray,
+        bottomspinecolor = :gray,
+        leftspinecolor = :gray,
+        rightspinecolor = :gray,
+        ylabel = "Time relative to C",
+        xticks = (1:length(unique(langs)), langs.pool.levels),
+        xminorticks = IntervalsBetween(2),
+        xgridvisible = false,
+        xminorgridvisible = true,
+        xminorgridcolor = (:black, 0.2),
+        yminorticks = IntervalsBetween(5),
+        yminorgridvisible = true,
+    ),
+    figure = (; size = (1000, 618),)
+)
+leg = Legend(f[1, 2],
+    [MarkerElement(; color = Makie.categorical_colors(:Set1_8, 8)[i], marker = :circle, markersize = 11) for i in 1:length(bms.pool.levels)],
+    bms.pool.levels,
+    "Benchmark";
+)
+f
+
+```
+
+
+## Benchmarks colored by language
+
+```@example julia-benchmark
+
+f, a, p = beeswarm(
+    bms.refs, benchmarks.normtime;
+    color = langs.refs,
+    colormap = Makie.Colors.distinguishable_colors(13),#:Set1_9,
+    # markersize = 5,
+    marker = Circle,
+    axis = (;
+        yscale = log10,
+        xticklabelrotation = 0, 
+        xticklabelsize = 12,
+        xticksvisible = false,
+        topspinecolor = :gray,
+        bottomspinecolor = :gray,
+        leftspinecolor = :gray,
+        rightspinecolor = :gray,
+        ylabel = "Time relative to C",
+        xticks = (1:length(unique(bms)), bms.pool.levels),
+        xminorticks = IntervalsBetween(2),
+        xgridvisible = false,
+        xminorgridvisible = true,
+        xminorgridcolor = (:black, 0.2),
+        yminorticks = IntervalsBetween(5),
+        yminorgridvisible = true,
+    ),
+    figure = (; size = (1000, 618),)
+)
+leg = Legend(f[1, 2],
+    [MarkerElement(; color = p.colormap[][i], marker = :circle, markersize = 11) for i in 1:length(langs.pool.levels)],
+    langs.pool.levels,
+    "Benchmark";
+)
+f
+```
+
+## Custom markers
+```@example julia-benchmark
+# Get logos for programming languages
+
+using Rsvg
+using CairoMakie
+using CairoMakie.Cairo, CairoMakie.FileIO
+
+function pngify(input_data::AbstractString)
+    r = Rsvg.handle_new_from_data(String(input_data));
+    Rsvg.handle_set_dpi(r, 2.0)
+    d = Rsvg.handle_get_dimensions(r);
+    img = fill(Makie.Colors.ARGB32(0, 0, 0, 0), d.width * 4, d.height * 4)
+    # create an image surface to draw onto the image
+    surf = Cairo.CairoImageSurface(img)
+    ctx = Cairo.CairoContext(surf);
+    Cairo.scale(ctx, 4, 4)
+    Rsvg.handle_render_cairo(ctx,r);
+    return permutedims(img)
+end
+
+
+language_logo_url(lang::String) = "https://cdn.jsdelivr.net/gh/devicons/devicon@latest/icons/$(lowercase(lang))/$(lowercase(lang))-original.svg"
+
+language_marker_dict = Dict(
+    [key => read(download(language_logo_url(key)), String) |> pngify for key in ("c", "fortran", "go", "java", "javascript", "julia", "matlab", "python", "r", "rust")]
+)
+
+language_marker_dict["octave"] = FileIO.load(File{format"PNG"}(download("https://upload.wikimedia.org/wikipedia/commons/thumb/6/6a/Gnu-octave-logo.svg/2048px-Gnu-octave-logo.svg.png"))) .|> Makie.Colors.ARGB32  
+
+language_marker_dict["luajit"] = read(download(language_logo_url("lua")), String) |> pngify 
+language_marker_dict["mathematica"] = read(download("https://upload.wikimedia.org/wikipedia/commons/2/20/Mathematica_Logo.svg"), String) |> pngify 
+
+
+f, a, p = beeswarm(
+    bms.refs, benchmarks.normtime;
+    marker = getindex.((language_marker_dict,),lowercase.(benchmarks.language)),
+    markersize = 11,
+    axis = (;
+        yscale = log10,
+        xticklabelrotation = 0, 
+        xticklabelsize = 12,
+        xticksvisible = false,
+        topspinecolor = :gray,
+        bottomspinecolor = :gray,
+        leftspinecolor = :gray,
+        rightspinecolor = :gray,
+        ylabel = "Time relative to C",
+        xticks = (1:length(unique(bms)), bms.pool.levels),
+        xminorticks = IntervalsBetween(2),
+        xgridvisible = false,
+        xminorgridvisible = true,
+        xminorgridcolor = (:black, 0.2),
+        yminorticks = IntervalsBetween(5),
+        yminorgridvisible = true,
+    ),
+    figure = (; size = (1000, 618),)
+)
+leg = Legend(f[1, 2],
+    [MarkerElement(; marker = language_marker_dict[lowercase(lang)], markersize = 15) for lang in langs.pool.levels],
+    langs.pool.levels,
+    "Language";
+)
+f
+```
diff --git a/src/algorithms/simple.jl b/src/algorithms/simple.jl
@@ -27,7 +27,12 @@ function calculate!(buffer::AbstractVector{<: Point2}, alg::SimpleBeeswarm, posi
 
     for x_val in unique(xs)
         group = findall(==(x_val), xs)
-        xs[group] .= simple_xs(view(ys, group), markersize, side)
+        view_ys = view(ys, group)
+        if isempty(view_ys)
+            continue
+        else
+            xs[group] .= simple_xs(view_ys, markersize, side)
+        end
     end
 
     buffer .= Point2f.(xs .+ first.(positions), last.(positions))

diff --git a/src/recipe.jl b/src/recipe.jl
@@ -99,20 +99,25 @@ function Makie.plot!(plot::Beeswarm)
     point_buffer = Observable{Vector{Point2f}}(zeros(Point2f, length(positions[])))
     pixelspace_point_buffer = Observable{Vector{Point2f}}(zeros(Point2f, length(positions[])))
     # when the positions change, we must update the buffer arrays
-    onany(plot, plot.converted[1], plot.algorithm, plot.color, plot.markersize, plot.side, plot.direction, plot.gutter, plot.gutter_threshold, should_update_based_on_zoom) do positions, algorithm, colors, markersize, side, direction, gutter, gutter_threshold, _
+    onany(plot, plot.converted[1], plot.algorithm, plot.transformation.transform_func, plot.markersize, plot.side, plot.direction, plot.gutter, plot.gutter_threshold, should_update_based_on_zoom) do positions, algorithm, tfunc, markersize, side, direction, gutter, gutter_threshold, _
         @assert side in (:both, :left, :right) "side should be one of :both, :left, or :right, got $(side)"
         @assert direction in (:x, :y) "direction should be one of :x or :y, got $(direction)"
         if length(positions) != length(point_buffer[])
             # recreate the point buffers if lengths have changed
             point_buffer.val = copy(positions)
             pixelspace_point_buffer.val = zeros(Point2f, length(positions))
         end
+        # Apply nonlinear transform function if any
+        pixelspace_point_buffer.val .= Makie.apply_transform(tfunc, positions, :data)
         # Project input positions from data space to pixel space
-        pixelspace_point_buffer.val .= Point2f.(Makie.project.((scene.camera,), :data, :pixel, direction == :y ? positions : reverse.(positions)))
+        pixelspace_point_buffer.val .= Point2f.(Makie.project.((scene.camera,), :data, :pixel, direction == :y ? pixelspace_point_buffer.val : reverse.(pixelspace_point_buffer.val)))
         # Calculate the beeswarm in pixel space and store it in `point_buffer.val`
         calculate!(point_buffer.val, algorithm, direction == :y ? pixelspace_point_buffer.val : reverse.(pixelspace_point_buffer.val), markersize, side)
         # Project the beeswarm back to data space and store it, again, in `point_buffer.val`
         point_buffer.val .= Point2f.(Makie.project.((scene.camera,), :pixel, :data, direction == :y ? (point_buffer.val) : reverse.(point_buffer.val)))
+        # Finally, apply the inverse transform to move back into data space.
+        # TODO: remove this once we have `space==:transformed` in Makie.
+        point_buffer.val .= Makie.apply_transform(Makie.inverse_transform(tfunc), point_buffer.val, :data)
 
         # Method to create a gutter when a gutter is defined
         # NOTE: Maybe turn this into a helper function?
@@ -187,4 +192,4 @@ function gutterize!(point_buffer, algorithm::BeeswarmAlgorithm, positions, direc
             """
         end
     end
-end
+end
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		# Scaled beeswarm plots

		Beeswarm plots can also be plotted in log-scale axes!