Merge pull request #169 from diegozea/dev

Arc and chord diagram

src/Plots.jl

@@ -127,7 +127,8 @@ export
     PlotRecipe,
     # EllipseRecipe,
     spy,
-    arcdiagram
+    arcdiagram,
+    chorddiagram
     # corrplot
 
 

src/recipes.jl

@@ -138,57 +138,11 @@ end
 
 abline!(args...; kw...) = abline!(current(), args...; kw...)
 
-# -------------------------------------------------
+# =================================================
-# Arc Diagram
+# Arc and chord diagrams
 
-curvecolor(value, min, max, grad) = getColorZ(grad, (value-min)/(max-min))
+"Takes an adjacency matrix and returns source, destiny and weight lists"
-
+function mat2list{T}(mat::AbstractArray{T,2})
-"Plots a clockwise arc, from source to destiny, colored by weight"
-function arc!(source, destiny, weight, min, max, grad)
-    radius = (destiny - source) / 2
-    arc = Plots.partialcircle(0, π, 30, radius)
-    x, y = Plots.unzip(arc)
-    plot!(x .+ radius .+ source,  y, line = (curvecolor(weight, min, max, grad), 0.5, 2))
-end
-
-"""
-`arcdiagram(source, destiny, weight[, grad])`
-
-Plots an arc diagram, form `source` to `destiny` (clockwise), using `weight` to determine the colors.
-"""
-function arcdiagram(source, destiny, weight, grad=ColorGradient(:bluesreds))
-
-    if length(source) == length(destiny) == length(weight)
-
-        vertices = vcat(source, destiny)
-
-        xmin, xmax = extrema(vertices)
-        plot(xlim=(xmin - 0.5, xmax + 0.5))
-
-        wmin,wmax = extrema(weight)
-
-        for (i, j, value) in zip(source,destiny,weight)
-            arc!(i, j, value, wmin, wmax, grad)
-        end
-
-        scatter!(vertices, zeros(length(vertices)), leg=false)
-
-        else
-
-        throw(ArgumentError("source, destiny and weight should have the same length"))
-
-    end
-end
-
-"""
-`arcdiagram(mat[, grad])`
-
-Plots an arc diagram of a matrix, form rows to columns (clockwise),
-using the values on the matrix as weights to determine the colors.
-Doesn't show edges with value zero if the input is sparse.
-For simmetric matrices, only the upper triangular values are used.
-"""
-function arcdiagram{T}(mat::AbstractArray{T,2}, grad=ColorGradient(:bluesreds))
     nrow, ncol = size(mat) # rows are sources and columns are destinies
 
     nosymmetric = !issym(mat) # plots only triu for symmetric matrices
@@ -220,9 +174,152 @@ function arcdiagram{T}(mat::AbstractArray{T,2}, grad=ColorGradient(:bluesreds))
         end
     end
 
-    resize!(source, idx-1)
+    resize!(source, idx-1), resize!(destiny, idx-1), resize!(weight, idx-1)
-    resize!(destiny, idx-1)
-    resize!(weight, idx-1)
-
-    arcdiagram(source, destiny, weight, grad)
 end
+
+# -------------------------------------------------
+# Arc Diagram
+
+curvecolor(value, min, max, grad) = getColorZ(grad, (value-min)/(max-min))
+
+"Plots a clockwise arc, from source to destiny, colored by weight"
+function arc!(source, destiny, weight, min, max, grad)
+    radius = (destiny - source) / 2
+    arc = Plots.partialcircle(0, π, 30, radius)
+    x, y = Plots.unzip(arc)
+    plot!(x .+ radius .+ source,  y, line = (curvecolor(weight, min, max, grad), 0.5, 2), legend=false)
+end
+
+"""
+`arcdiagram(source, destiny, weight[, grad])`
+
+Plots an arc diagram, form `source` to `destiny` (clockwise), using `weight` to determine the colors.
+"""
+function arcdiagram(source, destiny, weight; kargs...)
+
+    args = Dict(kargs)
+    grad = pop!(args, :grad,   ColorGradient([colorant"darkred", colorant"darkblue"]))
+
+    if length(source) == length(destiny) == length(weight)
+
+        vertices = unique(vcat(source, destiny))
+        sort!(vertices)
+
+        xmin, xmax = extrema(vertices)
+        plot(xlim=(xmin - 0.5, xmax + 0.5), legend=false)
+
+        wmin,wmax = extrema(weight)
+
+        for (i, j, value) in zip(source,destiny,weight)
+            arc!(i, j, value, wmin, wmax, grad)
+        end
+
+        scatter!(vertices, zeros(length(vertices)); legend=false, args...)
+
+    else
+
+        throw(ArgumentError("source, destiny and weight should have the same length"))
+
+    end
+end
+
+"""
+`arcdiagram(mat[, grad])`
+
+Plots an arc diagram from an adjacency matrix, form rows to columns (clockwise),
+using the values on the matrix as weights to determine the colors.
+Doesn't show edges with value zero if the input is sparse.
+For simmetric matrices, only the upper triangular values are used.
+"""
+arcdiagram{T}(mat::AbstractArray{T,2}; kargs...) = arcdiagram(mat2list(mat)...; kargs...)
+
+# -------------------------------------------------
+# Chord diagram
+
+arcshape(θ1, θ2) = Shape(vcat(Plots.partialcircle(θ1, θ2, 15, 1.1),
+                            reverse(Plots.partialcircle(θ1, θ2, 15, 0.9))))
+
+colorlist(grad, ::Void) = :darkgray
+
+function colorlist(grad, z)
+    zmin, zmax = extrema(z)
+    RGBA{Float64}[getColorZ(grad, (zi-zmin)/(zmax-zmin)) for zi in z]'
+end
+
+"""
+`chorddiagram(source, destiny, weight[, grad, zcolor, group])`
+
+Plots a chord diagram, form `source` to `destiny`,
+using `weight` to determine the edge colors using `grad`.
+`zcolor` or `group` can be used to determine the node colors.
+"""
+function chorddiagram(source, destiny, weight; kargs...)
+
+    args=Dict(kargs)
+    grad  = pop!(args, :grad,   ColorGradient([colorant"darkred", colorant"darkblue"]))
+    zcolor= pop!(args, :zcolor, nothing)
+    group = pop!(args, :group,  nothing)
+
+    if zcolor !== nothing && group !== nothing
+        throw(ErrorException("group and zcolor can not be used together."))
+    end
+
+    if length(source) == length(destiny) == length(weight)
+
+        plt = plot(xlim=(-2,2), ylim=(-2,2), legend=false, grid=false,
+        xticks=nothing, yticks=nothing,
+        xlim=(-1.2,1.2), ylim=(-1.2,1.2))
+
+        nodemin, nodemax = extrema(vcat(source, destiny))
+
+        weightmin, weightmax = extrema(weight)
+
+        A  = 1.5π # Filled space
+        B  = 0.5π # White space (empirical)
+
+        Δα = A / nodemax
+        Δβ = B / nodemax
+
+        δ = Δα  + Δβ
+
+        for i in 1:length(source)
+            curve = BezierCurve(P2[ (cos((source[i ]-1)*δ + 0.5Δα), sin((source[i ]-1)*δ + 0.5Δα)), (0,0),
+                                    (cos((destiny[i]-1)*δ + 0.5Δα), sin((destiny[i]-1)*δ + 0.5Δα)) ])
+            plot!(curve_points(curve), line = (Plots.curvecolor(weight[i], weightmin, weightmax, grad), 1, 1))
+        end
+
+        if group === nothing
+            c =  colorlist(grad, zcolor)
+        elseif length(group) == nodemax
+
+            idx = collect(0:(nodemax-1))
+
+            for g in group
+                plot!([arcshape(n*δ, n*δ + Δα) for n in idx[group .== g]]; args...)
+            end
+
+            return plt
+
+        else
+            throw(ErrorException("group should the ", nodemax, " elements."))
+        end
+
+        plot!([arcshape(n*δ, n*δ + Δα) for n in 0:(nodemax-1)]; mc=c, args...)
+
+        return plt
+
+    else
+        throw(ArgumentError("source, destiny and weight should have the same length"))
+    end
+end
+
+"""
+`chorddiagram(mat[, grad, zcolor, group])`
+
+Plots a chord diagram from an adjacency matrix,
+using the values on the matrix as weights to determine edge colors.
+Doesn't show edges with value zero if the input is sparse.
+For simmetric matrices, only the upper triangular values are used.
+`zcolor` or `group` can be used to determine the node colors.
+"""
+chorddiagram(mat::AbstractMatrix; kargs...) = chorddiagram(mat2list(mat)...; kargs...)