fixed plots

Project.toml

@@ -4,7 +4,7 @@ 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"
+version = "0.2.0"
 
 [deps]
 ComputationalHomology = "9393a4d0-be1e-45b0-9991-b60434c721e6"
@@ -17,6 +17,11 @@ Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
+[compat]
+MultivariateStats = "^0.7.0"
+ComputationalHomology = "^0.6.0"
+julia = "≥ 1.1.0"
+
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 

README.md

@@ -24,7 +24,8 @@ pkg> add TDA
 ```julia
 using TDA, ComputationalHomology, Plots
 # crate some intervals of various dimensions
-ints = vcat(intervals(0, 2.0=>6.0, 5.0=>10.0, 1.0=>Inf), intervals(1, 9.0=>12.0))
+ints = Dict(0=>diagram(2.0=>6.0, 5.0=>10.0, 1.0=>Inf), 1=>diagram(9.0=>12.0))
+
 # plot persistance diagram
 plot(ints)
 # plot barcode

src/graph.jl

@@ -1,7 +1,7 @@
 # Plot a 1D simplicial subcomplex (graph) of `cplx`
 @recipe function f(cplx::T, args...) where {T<:SimplicialComplex}
     data = length(args) > 0 ? args[1] :
-                              circlepoints(size(cplx, 0)+1, 1.0)
+                              hcat(circlepoints(size(cplx, 0)+1, 1.0)...)
     for (i,c) in enumerate(cells(cplx, 1))
         pts = data[values(c),:]
         @series begin

src/pdiag.jl

@@ -1,22 +1,17 @@
-@recipe function f(ints::Vector{Interval};
-                   maxoutdim=1,
-                   skipzero = false)
-    # get interval dimensions
-    dims = unique(map(i->i.dim, ints))
-    # group intervals by dimensions
-    Dict(d=>filter(i->i.dim==d, ints) for d in dims)
+@recipe function f(ints::Vector{T}) where {T<:AbstractInterval}
+    Dict(0=>ints)
 end
 
 # Plot intervals as a persistance diagram or barcode
-@recipe function f(grints::Dict{Int, Vector{Interval}};
+@recipe function f(dgm::Dict{Int, Vector{T}};
                    maxoutdim=1,
-                   skipzero = false)
+                   skipzero = false) where {T<:AbstractInterval}
     # set default plot type
     seriestype --> :diagram
 
     # get interval dimensions
-    vals = vcat(([i.b, i.d] for i in vcat(values(grints)...))...)
-    dims = [d for d in sort!(filter!(d->d<=maxoutdim, collect(keys(grints))))]
+    vals = vcat(([i.b, i.d] for i in vcat(values(dgm)...))...)
+    dims = [d for d in sort!(filter!(d->d<=maxoutdim, collect(keys(dgm))))]
     # compute range of intervals
     minval, maxval = extrema(filter!(!isinf, vals))
 
@@ -28,12 +23,13 @@ end
         legend := :none
         layout := (length(dims),1)
         for (pi, d) in enumerate(dims)
-            dmaxval = max(maxval, foldl(max, filter(!isinf, map(i->i.d, grints[d])); init=-Inf))
-            dminval = min(minval, foldl(min, filter(!isinf, map(i->i.b, grints[d])); init=Inf))
-            points = map(i -> i.b == i.d, grints[d])
-            step = 1 / (skipzero ? sum(.!points) : length(grints[d]))
+            dmaxval = max(maxval, foldl(max, filter(!isinf, map(i->i.d, dgm[d])); init=-Inf))
+            dminval = min(minval, foldl(min, filter(!isinf, map(i->i.b, dgm[d])); init=Inf))
+            points = map(i -> i.b == i.d, dgm[d])
+            step = 1 / (skipzero ? sum(.!points) : length(dgm[d]))
             y = step
-            for (i, ispoint) in zip(grints[d], points)
+            idxs = sortperm(dgm[d])
+            for (i, ispoint) in zip(dgm[d][idxs], points)
                 xs, ys = [i.b, isinf(i.d) ? maxval : i.d], [y, y]
                 ispoint && skipzero && continue
                 @series begin
@@ -53,17 +49,17 @@ end
         end
     else # Persistance Diagram
         padding = (maxval - minval)*0.01 # 3%
-        xs = map(l->map(i->i.b,l), grints[d] for d in dims)
-        ys = map(l->map(i->isinf(i.d) ? maxval : i.d,l), grints[d] for d in dims)
-        mkr = map(l->map(i->isinf(i.d) ? :rect : :circle,l), grints[d] for d in dims)
+        xs = map(l->map(i->i.b,l), dgm[d] for d in dims)
+        ys = map(l->map(i->isinf(i.d) ? maxval : i.d,l), dgm[d] for d in dims)
+        mkr = map(l->map(i->isinf(i.d) ? :rect : :circle,l), dgm[d] for d in dims)
         legend --> :bottomright
         legendtitle --> "Homology"
-        label --> ["Degree $(i-1)" for i in 1:length(grints)]
-        #xticks := minval:maxval
+        # label --> ["Degree $(i-1)" for i in 1:length(dgm)]
+        # xticks := minval:maxval
         xlims := (minval-padding, maxval+padding)
-        xlabel := "birth"
-        #yticks := 0:maxval
-        ylabel := "death"
+        xguide := "birth"
+        # yticks := 0:maxval
+        yguide := "death"
         ylims := (minval, maxval*1.03)
 
         @series begin
@@ -74,13 +70,14 @@ end
         end
 
         for i in 1:length(xs)
-            idxs = skipzero ? xs[i] .!== ys[i] : .!BitArray(undef, length(xs[i]))
+            idxs = skipzero ? xs[i] .!== ys[i] : BitArray(true for i in 1:length(xs[i]))
             @series begin
                 primary := true
                 seriestype := :scatter
                 markershape := mkr[i][idxs]
                 markersize --> 2
-                #markerstrokecolor := col
+                label --> "Degree $(i-1)"
+                # markerstrokecolor := col
                 xs[i][idxs], ys[i][idxs]
             end
         end