added persistance plots

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 Art
+Copyright (c) 2019 Art Wild
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Project.toml

@@ -0,0 +1,21 @@
+name = "TDA"
+uuid = "fe47203d-f35f-412c-997c-af2409ec39e9"
+keywords = ["topological data analysis", "data science", "persistance"]
+license = "MIT"
+desc = "A Julia package for topological data analysis"
+repository = "https://github.com/wildart/TDA.jl.git"
+version = "0.1.0"
+
+[deps]
+ComputationalHomology = "9393a4d0-be1e-45b0-9991-b60434c721e6"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
+RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]
+

src/TDA.jl

@@ -0,0 +1,8 @@
+module TDA
+
+using ComputationalHomology
+using RecipesBase
+
+include("pdiag.jl")
+
+end

src/pdiag.jl

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+# Plot intervals as a persistance diagram or barcode
+@recipe function f(ints::Vector{Vector{T}}; skipzero = false) where {T<:Interval}
+    seriestype --> :diagram
+
+    maxval = mapreduce(l->maximum(filter(!isinf, map(i->i.d,l))), max, ints)
+    minval = mapreduce(l->minimum(filter(!isinf, map(i->i.b,l))), min, ints)
+    #col = vcat(map(l->map(i->isinf(i.d) ? :red : :auto ,l), ints)...)
+
+    if plotattributes[:seriestype] == :barcode # Persistance Barcode
+        xticks := minval:maxval
+        xlims  := (minval, maxval+0.05)
+        yticks := nothing
+        ylims := (0.0, 1.05)
+        legend := :none
+        layout := (length(ints),1)
+        for d in 1:length(ints)
+            points = map(i -> i.b == i.d, ints[d])
+            step = 1 / (skipzero ? sum(.!points) : length(ints[d]))
+            y = step
+            for (i, ispoint) in zip(ints[d], points)
+                xs, ys = [i.b, isinf(i.d) ? maxval : i.d], [y, y]
+                println("ispoint: $ispoint")
+                println(!ispoint && skipzero)
+                ispoint && skipzero && continue
+                @series begin
+                    title := "Degree $(d-1)"
+                    linewidth --> 2
+                    subplot := d
+                    primary := true
+                    arrow := isinf(i.d)
+                    seriescolor --> :blue
+                    seriestype := ispoint ? :scatter : :path
+                    markersize --> 2
+                    xs, ys
+                end
+                y += step
+            end
+        end
+    else # Persistance Diagram
+        xs = map(l->map(i->i.b,l), ints)
+        ys = map(l->map(i->isinf(i.d) ? maxval : i.d,l), ints)
+        mkr = vcat(map(l->map(i->isinf(i.d) ? :rect : :circle,l), ints)...)
+        legend --> :bottomright
+        legendtitle --> "Homology"
+        label --> ["Degree $(i-1)" for i in 1:length(ints)]
+        xticks := minval:maxval
+        xlims := (minval-0.3, maxval+0.3)
+        xlabel := "birth"
+        yticks := 0:maxval
+        ylabel := "death"
+        ylims := (minval, maxval+0.3)
+        @series begin
+            primary := false
+            seriestype := :path
+            linecolor := :black
+            [0, maxval], [0, maxval]
+        end
+
+        seriestype := :scatter
+        markershape := mkr
+        #markerstrokecolor := col
+        xs, ys
+    end
+end