Skeleton of Seaborn algorithm

src/SwarmMakie.jl

@@ -7,5 +7,6 @@ using Makie, Random
 include("recipe.jl")
 include("algorithms/simple.jl")
 include("algorithms/mkborregaard.jl")
+include("algorithms/seaborn.jl")
 
 end

src/algorithms/seaborn.jl

@@ -0,0 +1,165 @@
+# # Seaborn algorithm
+
+export SeabornBeeswarm
+
+#=
+
+This code is adapted from the `seaborn` Python package,
+which is licensed under the BSD-3 license below:
+
+```md
+Copyright (c) 2012-2023, Michael L. Waskom All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+Neither the name of the project nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+```
+=#
+
+"""
+    SeabornBeeswarm()
+
+A beeswarm algorithm based on the `seaborn` Python package.  
+
+More adaptive to marker size than `SimpleBeeswarm`, 
+but takes longer to compute.
+"""
+struct SeabornBeeswarm <: BeeswarmAlgorithm end
+
+function SwarmMakie.calculate!(buffer::AbstractVector{<: Point2}, alg::SeabornBeeswarm, positions::AbstractVector{<: Point2}, markersize)
+    markersizes = if length(markersize) != length(positions)
+        fill(markersize, length(positions))
+    else
+        markersize
+    end
+
+    buffer .= _seaborn_beeswarm_xy(positions, markersizes)
+
+end
+
+
+function _seaborn_beeswarm_xy(positions, markersizes)
+    midline = first(positions)[1]
+
+    new_xy = Vector{Point2f}()
+    # We have to keep track of the indices, since we can't 
+    # re-order the markersize array.
+    new_idxs = Vector{Int}()
+    for (idx, (position, markersize)) in enumerate(zip(positions, markersizes))
+
+        neighbors = could_overlap(position, markersize, positions, markersizes)
+
+        candidate_positions, candidate_idxs = position_candidates(position, markersize, idx, neighbors, positions, markersizes)
+
+        # Sort candidates by centrality
+        offsets = abs.(first.(candidate_positions) .- midline)
+        candidate_permutation = sortperm(offsets)
+        candidate_positions = candidate_positions[candidate_permutation]
+        candidate_idxs = candidate_idxs[candidate_permutation]
+
+        new_position, new_idx = first_non_overlapping_candidate(position, markersize, idx, neighbors, candidate_idxs,candidate_positions, positions, markersizes)
+
+        push!(new_xy, new_position)
+        push!(new_idxs, new_idx)
+    end
+
+    gutterize!(new_xy, markersizes, midline, 7 * maximum(last.(markersizes)))
+
+    return new_xy[new_idxs]
+
+end
+
+"""
+    could_overlap(position, markersize, positions, markersizes)
+
+Check if a point given by `position` with markersize `markersize` could overlap with any other point in the swarm.
+Returns a vector of integer indices.
+"""
+function could_overlap(position::Point2, markersize, positions::AbstractVector{<: Point2}, markersizes::AbstractVector)
+    potential_neighbors = []
+    for (idx, (pos, msize)) in Iterators.reverse(enumerate(zip(positions, markersizes)))
+        if abs(position[2] - pos[2]) < (last(msize) + last(markersize)) / 2 # || abs(position[1] - pos[1]) < (first(msize) + first(markersize)) / 2
+            push!(potential_neighbors, idx)
+        end
+    end
+    return potential_neighbors
+end
+
+"""
+Returns `(positions::Vector{Point2f}, idxs::Vector{Int})`.
+"""
+function position_candidates(position, markersize, idx, neighbors, positions, markersizes)
+    candidate_positions = [position]
+    candidate_idxs = [idx]
+    left_first = true
+
+    for idx in neighbors
+        pos = positions[idx]
+        ms = markersizes[idx]
+        dy = position[2] - pos[2]
+        dx = √(max(0, (last(markersize) + last(ms)) ^ 2 - dy ^ 2)) * 1.05
+        pl, pr = Point2f(pos[1] - dx, pos[2]), Point2f(pos[1] + dx, pos[2])
+        if left_first
+            push!(candidate_positions, pl)
+            push!(candidate_positions, pr)
+            push!(candidate_idxs, idx)
+            push!(candidate_idxs, idx)
+        else
+            push!(candidate_positions, pr)
+            push!(candidate_positions, pl)
+            push!(candidate_idxs, idx)
+            push!(candidate_idxs, idx)
+        end
+        left_first = !left_first
+    end
+    return (candidate_positions, candidate_idxs)
+end
+
+"""
+    Returns `(position::Point2f, idx::Int)`
+"""
+function first_non_overlapping_candidate(position, markersize, idx, neighbor_idxs, candidate_idxs, candidate_positions, positions, markersizes)
+    if length(neighbor_idxs) == 1
+        return position, idx
+    end
+
+    neighbor_positions = view(positions, neighbor_idxs)
+    neighbor_ms = last.(markersizes[neighbor_idxs])
+
+    for (candidate_idx, candidate_position) in zip(candidate_idxs, candidate_positions)
+        # We don't need a square root, since we're comparing to another distance measure.
+        distances_to_points = sum.(map(x -> x .^ 2, (neighbor_positions .- candidate_position)))
+
+        separation_needed = (neighbor_ms .+ markersizes[candidate_idx]) .^ 2
+
+        if all(distances_to_points .>= separation_needed)
+            return positions[candidate_idx], candidate_idx
+        end
+    end
+    error("No non-overlapping candidate found - this should not happen!")
+end
+
+function gutterize!(positions, markersizes, center, width = 6 * maximum(last.(markersizes)))
+    low_gutter = center - width
+    high_gutter = center + width
+
+    off_low = first.(positions) .< low_gutter
+    off_high = first.(positions) .> high_gutter
+
+    positions[off_low] .= (low_gutter, last.(positions[off_low]))
+    positions[off_high] .= (high_gutter, last.(positions[off_high]))
+
+    gutter_proportion = (sum(off_low) + sum(off_high)) / length(positions)
+    if gutter_proportion > 0.05
+        @warn """
+        SwarmMakie: $(Makie.Format.format("{:.1%}", gutter_proportion)) of the points could not be placed within the width limits.
+        You may want to decrease the markersize.
+        """
+    end
+end

src/algorithms/wilkinson.jl

@@ -1,4 +1,4 @@
-# # Simple beeswarm
+# # Wilkinson beeswarm
 
 export WilkinsonBeeswarm