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Attribute forwarding update for Makie 0.21 (#99)
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* separate out handling of kwargs forwarded to individual component plots

* tests + fix

* pull out test setup into own file

* compat + version bump
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@palday
palday authored Aug 1, 2024
1 parent fb67cbb commit 2c412a5
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Showing 6 changed files with 88 additions and 135 deletions.
4 changes: 2 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "MixedModelsMakie"
uuid = "b12ae82c-6730-437f-aff9-d2c38332a376"
authors = ["Phillip Alday <[email protected]>", "Douglas Bates <[email protected]>", "contributors"]
version = "0.4.3"
version = "0.4.4"

[deps]
BSplineKit = "093aae92-e908-43d7-9660-e50ee39d5a0a"
Expand All @@ -19,7 +19,7 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
[compat]
Aqua = "0.5, 0.6"
BSplineKit = "0.15, 0.16, 0.17"
CairoMakie = "0.11"
CairoMakie = "0.11, 0.12"
DataFrames = "1"
Distributions = "0.25"
KernelDensity = "0.6.3"
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17 changes: 13 additions & 4 deletions src/coefplot.jl
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Expand Up @@ -3,13 +3,20 @@
coefplot!(fig::$(Indexable), x::Union{MixedModel,MixedModelBootstrap};
kwargs...)
coefplot!(ax::Axis, Union{MixedModel,MixedModelBootstrap};
conf_level=0.95, vline_at_zero=true, show_intercept=true, attributes...)
conf_level=0.95, vline_at_zero=true, show_intercept=true,
scatter_attributes=(;),
errorbars_attributes=(;),
attributes...)
Create a coefficient plot of the fixed-effects and associated confidence intervals.
Inestimable coefficients (coefficients removed by pivoting in the rank deficient case) are excluded.
`attributes` are passed onto `scatter!` and `errorbars!`.
`attributes` are passed onto both `scatter!` and `errorbars!`, while
`scatter_attributes` and `errorbars_attributes` are passed only onto `scatter!` and
`errorbars!`, respectively. (Starting with Makie 0.21, unsupported attributes for a
given plottype are no longer silently ignored, so it's necessary so separate out the
attributes that are only valid for a single plot type.)
The mutating methods return the original object.
Expand All @@ -36,6 +43,8 @@ function coefplot!(ax::Axis, x::Union{MixedModel,MixedModelBootstrap};
conf_level=0.95,
vline_at_zero=true,
show_intercept=true,
scatter_attributes=(;),
errorbars_attributes=(;),
attributes...)
ci = confint_table(x, conf_level; show_intercept)
y = nrow(ci):-1:1
Expand All @@ -44,9 +53,9 @@ function coefplot!(ax::Axis, x::Union{MixedModel,MixedModelBootstrap};

ax.xlabel = xlabel

scatter!(ax, xvals, y; attributes...)
scatter!(ax, xvals, y; attributes..., scatter_attributes...)
errorbars!(ax, xvals, y, xvals .- ci.lower, ci.upper .- xvals;
direction=:x, attributes...)
direction=:x, attributes..., errorbars_attributes...)
vline_at_zero && vlines!(ax, 0; color=(:black, 0.75), linestyle=:dash)

reset_limits!(ax)
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97 changes: 20 additions & 77 deletions src/ridge.jl
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Expand Up @@ -3,7 +3,12 @@
ridgeplot!(fig::$(Indexable), x::Union{MixedModel,MixedModelBootstrap};
kwargs...)
ridgeplot!(ax::Axis, Union{MixedModel,MixedModelBootstrap};
conf_level=0.95, vline_at_zero=true, show_intercept=true, attributes...)
conf_level=0.95, vline_at_zero=true, show_intercept=true,
scatter_attributes=(;),
errorbars_attributes=(;),
band_attributes=(;),
lines_attributes=(;),
attributes...)
Create a ridge plot for the bootstrap samples of the fixed effects.
Expand All @@ -13,6 +18,12 @@ The highest density interval corresponding to `conf_level` is marked with a bar
Setting `conf_level=missing` removes the markings for the highest density interval.
`attributes` are passed onto [`coefplot`](@ref), `band!` and `lines!`.
`scatter_attributes` and `errorbars_attributes` are passed only onto [`coefplot`](@ref).
`band_attributes` and `lines_attributes` are passed only onto `band!` and
`linesbars!`, respectively.
(Starting with Makie 0.21, unsupported attributes for a
given plottype are no longer silently ignored, so it's necessary so separate out the
attributes that are only valid for a single plot type.)
The mutating methods return the original object.
Expand Down Expand Up @@ -47,6 +58,10 @@ function ridgeplot!(ax::Axis, x::MixedModelBootstrap;
conf_level=0.95,
vline_at_zero=true,
show_intercept=true,
scatter_attributes=(;),
errorbars_attributes=(;),
band_attributes=(;),
lines_attributes=(;),
attributes...)
xlabel = if !ismissing(conf_level)
@sprintf "Normalized bootstrap density and %g%% confidence interval" (conf_level *
Expand All @@ -57,11 +72,11 @@ function ridgeplot!(ax::Axis, x::MixedModelBootstrap;

if !ismissing(conf_level)
coefplot!(ax, x; conf_level, vline_at_zero, show_intercept, color=:black,
attributes...)
scatter_attributes, errorbars_attributes, attributes...)
end

attributes = merge((; color=:black), attributes)
band_attributes = merge(attributes, (; color=(_color(attributes.color), 0.3)))
band_attributes = merge((; color=(_color(attributes.color), 0.3)), band_attributes)

ax.xlabel = xlabel

Expand All @@ -78,8 +93,8 @@ function ridgeplot!(ax::Axis, x::MixedModelBootstrap;
dd = 0.95 * row.kde.density ./ maximum(row.kde.density)
lower = Point2f.(row.kde.x, offset)
upper = Point2f.(row.kde.x, dd .+ offset)
band!(ax, lower, upper; band_attributes...)
lines!(ax, upper; attributes...)
band!(ax, lower, upper; attributes..., band_attributes...)
lines!(ax, upper; attributes..., lines_attributes...)
end

# check conf_level so that we don't double print
Expand All @@ -96,75 +111,3 @@ function ridgeplot!(ax::Axis, x::MixedModelBootstrap;

return ax
end

# """
# ridgeplot!(ax::Axis, df::AbstractDataFrame, densvar::Symbol, group::Symbol; normalize=false)
# ridgeplot!(f::Union{Makie.FigureLike,Makie.GridLayout}, args...; pos=(1,1) kwargs...)
# ridgeplot(args...; kwargs...)

# Create a "ridge plot".

# A ridge plot is stacked plot of densities for a given variable (`densvar`) grouped by a different variable (`group`). Because densities can very widely in scale, it is sometimes useful to `normalize` the densities so that each density has a maximum of 1.

# The non-mutating method creates a Figure before calling the method for Figure.
# The method for Figure places the ridge plot in the grid position specified by `pos`, default is (1,1).
# """
# function ridgeplot!(ax::Axis, df::AbstractDataFrame, densvar::Symbol, group::Symbol; sort_by_group=false, vline_at_zero=true, normalize=false)
# # `normalize` makes it so that the max density is always 1
# # `normalize` works on the density not the area/mass
# gdf = groupby(df, group)
# dens = combine(gdf, densvar => kde => :kde)
# sort_by_group && sort!(dens, group)
# spacing = normalize ? 1.0 : 0.9 * maximum(dens[!, :kde]) do val
# return maximum(val.density)
# end

# nticks = length(gdf)

# for (idx, row) in enumerate(eachrow(dens))
# dd = normalize ? row.kde.density ./ maximum(row.kde.density) : row.kde.density

# offset = idx * spacing

# lower = Node(Point2f.(row.kde.x, offset))
# upper = Node(Point2f.(row.kde.x, dd .+ offset))
# band!(ax, lower, upper; color=(:black, 0.3))
# lines!(ax, upper; color=(:black, 1.0))
# end

# vline_at_zero && vlines!(ax, 0; color=(:black, 0.75), linestyle=:dash)

# ax.yticks[] = (1:spacing:(nticks*spacing), string.(dens[!, group]))
# ylims!(ax, 0, (nticks + 2) * spacing)
# ax.xlabel[] = string(densvar)
# ax.ylabel[] = string(group)

# ax
# end

# function ridgeplot!(f::Union{Makie.FigureLike,Makie.GridLayout}, args...; pos=(1,1), kwargs...)
# ridgeplot!(Axis(f[pos...]), args...; kwargs...)
# return f
# end

# """
# ridgeplot(args...; kwargs...)

# See [ridgeplot!](@ref).
# """
# ridgeplot(args...; kwargs...) = ridgeplot!(Figure(), args...; kwargs...)

# """
# ridgeplot!(Union{Figure, Axis}, bstrp::MixedModelBootstrap, args...; show_intercept=true, kwargs...)
# ridgeplot(bstrp::MixedModelBootstrap, args...; show_intercept=true, kwargs...)

# Convenience methods that call `DataFrame(bstrp.β)` and pass that onto the primary `ridgeplot[!]` methods.
# By default, the intercept is shown, but this can be disabled.
# """
# function ridgeplot!(axis::Axis, bstrp::MixedModelBootstrap, args...;
# show_intercept=true, normalize=true, kwargs...)

# df = DataFrame(bstrp.β)
# show_intercept || filter!(:coefname => !=(Symbol("(Intercept)")), df)
# ridgeplot!(axis, df, :β, :coefname, args...; sort_by_group=false, normalize, kwargs...)
# end
2 changes: 1 addition & 1 deletion test/ridgeplot.jl
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
f = ridgeplot(b1)
@test save(joinpath(OUTDIR, "ridge_sleepstudy.png"), f)

f = ridgeplot(br)
f = ridgeplot(br; color=(:blue, 0.3), errorbars_attributes=(; whiskerwidth=15))
@test save(joinpath(OUTDIR, "ridge_rankdeficient.png"), f)
52 changes: 1 addition & 51 deletions test/runtests.jl
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@@ -1,54 +1,4 @@
using Aqua
using CairoMakie
using DataFrames
using MixedModels
using MixedModelsMakie
using Random # we don't depend on exact PRNG vals, so no need for StableRNGs
using Statistics
using Suppressor
using Test
using TestSetExtensions

using MixedModelsMakie: confint_table

const OUTDIR = joinpath(pkgdir(MixedModelsMakie), "test", "output")
const progress = false

function save(path, obj, args...; kwargs...)
isfile(path) && rm(path)
Makie.save(path, obj, args...; kwargs...)
return isfile(path)
end

m1 = fit(MixedModel,
@formula(1000 / reaction ~ 1 + days + (1 + days | subj)),
MixedModels.dataset(:sleepstudy); progress)

m1zc = fit(MixedModel,
@formula(1000 / reaction ~ 1 + days + zerocorr(1 + days | subj)),
MixedModels.dataset(:sleepstudy); progress)

m2 = fit(MixedModel,
@formula(rt_trunc ~ 1 + spkr * prec * load +
(1 + spkr + prec + load | subj) +
(1 + spkr | item)),
MixedModels.dataset(:kb07); progress)

b1 = parametricbootstrap(MersenneTwister(42), 500, m1; progress,
optsum_overrides=(; ftol_rel=1e-6))
g1 = fit(MixedModel,
@formula(r2 ~ 1 + anger + gender + btype + situ +
(1 | subj) + (1 + gender | item)),
MixedModels.dataset(:verbagg),
Bernoulli(); progress)

rng = MersenneTwister(0)
x = rand(rng, 100)
a = rand(rng, 100)
data = (; x, x2=1.5 .* x, a, y=rand(rng, [0, 1], 100), g=repeat('A':'T', 5))
mr = @suppress fit(MixedModel, @formula(y ~ a + x + x2 + (1 | g)), data; progress)
br = @suppress parametricbootstrap(MersenneTwister(42), 500, mr; progress,
optsum_overrides=(; ftol_rel=1e-6))
include("setup_tests.jl")

@testset ExtendedTestSet "MixedModelsMakie.jl" begin
@testset "Aqua" begin
Expand Down
51 changes: 51 additions & 0 deletions test/setup_tests.jl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@
using Aqua
using CairoMakie
using DataFrames
using MixedModels
using MixedModelsMakie
using Random # we don't depend on exact PRNG vals, so no need for StableRNGs
using Statistics
using Suppressor
using Test
using TestSetExtensions

using MixedModelsMakie: confint_table

const OUTDIR = joinpath(pkgdir(MixedModelsMakie), "test", "output")
const progress = false

function save(path, obj, args...; kwargs...)
isfile(path) && rm(path)
Makie.save(path, obj, args...; kwargs...)
return isfile(path)
end

m1 = fit(MixedModel,
@formula(1000 / reaction ~ 1 + days + (1 + days | subj)),
MixedModels.dataset(:sleepstudy); progress)

m1zc = fit(MixedModel,
@formula(1000 / reaction ~ 1 + days + zerocorr(1 + days | subj)),
MixedModels.dataset(:sleepstudy); progress)

m2 = fit(MixedModel,
@formula(rt_trunc ~ 1 + spkr * prec * load +
(1 + spkr + prec + load | subj) +
(1 + spkr | item)),
MixedModels.dataset(:kb07); progress)

b1 = parametricbootstrap(MersenneTwister(42), 500, m1; progress,
optsum_overrides=(; ftol_rel=1e-6))
g1 = fit(MixedModel,
@formula(r2 ~ 1 + anger + gender + btype + situ +
(1 | subj) + (1 + gender | item)),
MixedModels.dataset(:verbagg),
Bernoulli(); progress)

rng = MersenneTwister(0)
x = rand(rng, 100)
a = rand(rng, 100)
data = (; x, x2=1.5 .* x, a, y=rand(rng, [0, 1], 100), g=repeat('A':'T', 5))
mr = @suppress fit(MixedModel, @formula(y ~ a + x + x2 + (1 | g)), data; progress)
br = @suppress parametricbootstrap(MersenneTwister(42), 500, mr; progress,
optsum_overrides=(; ftol_rel=1e-6))

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@palday palday commented on 2c412a5 Aug 1, 2024

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Registration pull request created: JuliaRegistries/General/112242

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Release notes:

## Breaking changes

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