plot recipes for marginal histograms

added plots example into docs

format

add RecipesBase

actually add file...

formatting...

rm "using plots"

format...

Project.toml

@@ -12,6 +12,7 @@ MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 SCS = "c946c3f1-0d1f-5ce8-9dea-7daa1f7e2d13"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

docs/src/parameter_distributions.md

@@ -49,6 +49,27 @@ The use case `constrained_gaussian()` addresses is when prior information is qua
 
 The parameters of the Gaussian are chosen automatically (depending on the constraint) to reproduce the desired μ and σ — per the use case, other details of the form of the prior distribution shouldn't be important for downstream inference!
 
+### Plotting
+
+For quick visualization we have a plot recipe for `ParameterDistribution` types. This will plot marginal histograms for all dimensions of the parameter distribution. For example, 
+
+```@example snip1
+# with values:
+# e.g. lower_bound = 0.0, upper_bound = 1.0
+# μ_1 = 0.5, σ_1 = 0.25
+# μ_2 = 0.5, σ_2 = 0.25
+
+using Plots
+plot(prior) 
+```
+One can also access the underlying Gaussian distributions in the unconstrained space with
+
+```@example snip1
+using Plots
+plot(prior, constrained=false) 
+```
+
+
 ### Recommended constructor - Simple example
 
 Task: We wish to create a prior for a one-dimensional parameter. Our problem dictates that this parameter is bounded between 0 and 1; domain knowledge leads us to expect it should be around 0.7. The parameter is called `point_seven`.
@@ -387,10 +408,10 @@ name2 = "constrained_sampled"
 nothing # hide
 ```
 
-The final parameter is 20-dimensional, defined as a list of i.i.d univariate distributions we make use of the `VectorOfParameterized` type
+The final parameter is 4-dimensional, defined as a list of i.i.d univariate distributions we make use of the `VectorOfParameterized` type
 ```@example snip5
-d3 = VectorOfParameterized(repeat([Beta(2,2)],20))
-c3 = repeat([no_constraint()],20)
+d3 = VectorOfParameterized(repeat([Beta(2,2)],4))
+c3 = repeat([no_constraint()],4)
 name3 = "Beta"
 nothing # hide
 ```
@@ -413,6 +434,16 @@ u = ParameterDistribution([param_dict1, param_dict2, param_dict3])
 nothing # hide
 ```
 
+We can visualize the marginals of the constrained distributions,
+```@example snip5
+using Plots
+plot(u)
+```
+and the unconstrained distributions similarly,
+```@example snip5
+using Plots
+plot(u, constrained = false)
+```
 
 ## ConstraintType Examples
 

src/EnsembleKalmanProcesses.jl

@@ -12,4 +12,6 @@ include("TOMLInterface.jl")
 # algorithmic updates
 include("EnsembleKalmanProcess.jl")
 
+# Plot recipes
+include("PlotRecipes.jl")
 end # module

src/PlotRecipes.jl

@@ -0,0 +1,86 @@
+module PlotRecipes
+
+using RecipesBase
+using Random
+using ..ParameterDistributions
+
+export plot_marginal_hist
+
+@recipe function plot(pd::ParameterDistribution; constrained = true, n_sample = 1e4, rng = Random.GLOBAL_RNG)
+    samples = sample(rng, pd, Int(n_sample))
+    if constrained
+        samples = transform_unconstrained_to_constrained(pd, samples)
+    end
+
+    # First attempt,  make it into a samples dist and plot histograms instead
+    n_plots = ndims(pd)
+    batches = batch(pd)
+
+    rows = Int(ceil(sqrt(n_plots)))
+    cols = Int(floor(sqrt(n_plots)))
+    tfs = 16
+    fs = 14
+
+    # subplot attr
+    legend := false
+    framestyle := repeat([:axes], n_plots)
+    grid := false
+
+    layout := n_plots
+    size --> (rows * 400, cols * 400)
+    titlefontsize --> tfs
+    xtickfontsize --> fs
+    ytickfontsize --> fs
+    xguidefontsize --> fs
+    yguidefontsize --> fs
+
+    for i in 1:n_plots
+        batch_id = [j for j = 1:length(batches) if i ∈ batches[j]][1]
+        dim_in_batch = i - minimum(batches[batch_id]) + 1 # i.e. if i=5 in batch 3:6, this would be "3"
+        @series begin
+            seriestype := :histogram
+            color := batch_id
+            subplot := i
+            title := pd.name[batch_id] * " (dim " * string(dim_in_batch) * ")"
+            samples[i, :]
+        end
+    end
+
+end
+
+@recipe function plot(d::PDT; n_sample = 1e4, rng = Random.GLOBAL_RNG) where {PDT <: ParameterDistributionType}
+    samples = sample(rng, d, Int(n_sample))
+
+    # First attempt,  make it into a samples dist and plot histograms instead
+    n_plots = ndims(d)
+
+    size_l = Int(ceil(sqrt(n_plots)))
+    tfs = 16
+    fs = 14
+
+    # subplot attr
+    legend := false
+    framestyle := repeat([:axes], n_plots)
+    grid := false
+    layout := n_plots
+    size --> (size_l * 400, size_l * 400)
+    titlefontsize --> tfs
+    xtickfontsize --> fs
+    ytickfontsize --> fs
+    xguidefontsize --> fs
+    yguidefontsize --> fs
+
+    for i in 1:n_plots
+        @series begin
+            seriestype := :histogram
+            subplot := i
+            title := "dim " * string(i)
+            samples[i, :]
+        end
+    end
+
+end
+
+
+
+end #module

test/PlotRecipes/runtests.jl

@@ -0,0 +1,47 @@
+using Test
+using Distributions
+using LinearAlgebra
+using Random
+using StatsBase
+
+using EnsembleKalmanProcesses.ParameterDistributions
+using EnsembleKalmanProcesses.PlotRecipes
+
+if TEST_PLOT_OUTPUT
+    @testset "PlotRecipes" begin
+        @testset "Plot ParameterDistribution" begin
+            d1 = Parameterized(MvNormal(zeros(4), 0.1 * I))
+            c1 = [no_constraint(), bounded_below(-1.0), bounded_above(0.4), bounded(-0.1, 0.2)]
+            name1 = "constrained_mvnormal"
+            u1 = ParameterDistribution(d1, c1, name1)
+
+            d2 = Samples([1 2 3 4])
+            c2 = [bounded(10, 15)]
+            name2 = "constrained_sampled"
+            u2 = ParameterDistribution(d2, c2, name2)
+
+            d3 = VectorOfParameterized(repeat([Beta(2, 2)], 3))
+            c3 = repeat([no_constraint()], 3)
+            name3 = "vector_beta"
+            u3 = ParameterDistribution(d3, c3, name3)
+
+            u = combine_distributions([u1, u2, u3])
+
+            # PDTs
+            plt1 = plot(d1)
+            savefig(plt1, joinpath(@__DIR__, name1 * ".png"))
+            plt2 = plot(d2)
+            savefig(plt2, joinpath(@__DIR__, name2 * ".png"))
+            plt3 = plot(d3)
+            savefig(plt3, joinpath(@__DIR__, name3 * ".png"))
+
+            # full param dist
+            plt_constrained = plot(u)
+            savefig(plt_constrained, joinpath(@__DIR__, "full_dist_constrained.png"))
+            plt_unconstrained = plot(u, constrained = false)
+            savefig(plt_unconstrained, joinpath(@__DIR__, "full_dist_unconstrained.png"))
+            # just a redundant test to show that the plots were created
+            @test 1 == 1
+        end
+    end
+end

test/runtests.jl

@@ -27,6 +27,7 @@ end
     for submodule in [
         "DataContainers",
         "ParameterDistributions",
+        "PlotRecipes",
         "Observations",
         "EnsembleKalmanProcess",
         "Localizers",