fixes

Author: jfb-h

Project.toml

@@ -7,6 +7,7 @@ version = "0.1.0"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
+Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
 
 [compat]
 julia = "1"

src/CitationNetworks.jl

@@ -18,7 +18,7 @@ include("mainpath_gbfp.jl")
 include("genetic_knowper.jl")
 include("convenience.jl")
 
-export compute_weights_spc, add_weights
+export weights_spc, add_weights
 export mainpath, ForwardLocal, BackwardLocal, StandardGlobal, GBFP
 export genetic_knowper
 export set_mp_prop!

src/convenience.jl

@@ -7,8 +7,8 @@ function set_mp_prop!(g::MetaDiGraph{T, U}, mp::MainPathResult, sym::Symbol) whe
         [set_prop!(g, v, sym, true) for v in vmp]
 end
 
-function add_weights(g::SimpleDiGraph{T}, weights::Vector{U}) where T <: Integer where U <: Real
-    from = [src(e) for e in edges(g)]
-    to = [dst(e) for e in edges(g)]
-    SimpleWeightedDiGraph(from, to, weights)
-end
+# function add_weights(g::SimpleDiGraph{T}, weights::Vector{U}) where T <: Integer where U <: Real
+#     from = [src(e) for e in edges(g)]
+#     to = [dst(e) for e in edges(g)]
+#     SimpleWeightedDiGraph(from, to, weights)
+# end

src/mainpath_gbfp.jl

@@ -28,10 +28,11 @@ function mainpath(
     gkp = genetic_knowper(g, normalize=normalize)
     start = findall(gkp .>= cutoff)
 
-    edges = Vector{SimpleEdge{T}}()
-    state = MainPathState(edges)
-    traverse_graph!(g, start, BreadthFirst(neighborfn = (g, v) -> vmax_outneighbors(g, v, gkp)), state) 
-    traverse_graph!(g, start, BreadthFirst(neighborfn = (g, v) -> vmax_outneighbors(g, v, gkp)), state) 
+    forwardstate = MainPathState(Vector{SimpleEdge{T}}())
+    backwardstate = MainPathState(Vector{SimpleEdge{T}}())
+    traverse_graph!(g, start, BreadthFirst(neighborfn = (g, v) -> vmax_outneighbors(g, v, gkp)), forwardstate) 
+    traverse_graph!(g, start, BreadthFirst(neighborfn = (g, v) -> vmax_inneighbors(g, v, gkp)), backwardstate) 
 
-    return GBFPResult(state.edges)
+    combined = vcat(forwardstate.edges, reverse.(backwardstate.edges)) |> unique
+    return GBFPResult(combined)
 end

src/weights_spc.jl

@@ -18,7 +18,7 @@ add_source_target! = function(g::AbstractGraph{T}) where T <: Integer
 end
 
 
-compute_weights_spc = function(g::AbstractGraph{T}; normalize = false) where T <: Integer
+weights_spc = function(g::AbstractGraph{T}; normalize = false) where T <: Integer
 
     N⁻ = function(g::SimpleDiGraph{T}, vseqt::Vector{T}) where T <: Integer
         nV = length(vseqt)

test/demo.jl

@@ -0,0 +1,76 @@
+### A Pluto.jl notebook ###
+# v0.11.14
+
+using Markdown
+using InteractiveUtils
+
+# ╔═╡ 0120e370-f8f5-11ea-1b65-9d29b0b5b647
+begin
+	using LightGraphs
+	using LightGraphs.SimpleGraphs
+	using MetaGraphs
+	using CitationNetworks
+	using GraphPlot
+end
+
+# ╔═╡ 0ba77020-f8f5-11ea-025d-61768c938c5c
+A = [
+ 0  0  1  0  0  0  0  0  0  0  0
+ 0  0  1  1  0  0  0  0  0  0  0
+ 0  0  0  0  1  0  1  0  0  0  0
+ 0  0  0  0  0  1  0  0  0  1  1
+ 0  0  0  0  0  0  0  1  1  0  0
+ 0  0  0  0  0  0  0  0  1  1  0
+ 0  0  0  0  0  0  0  0  0  0  0
+ 0  0  0  0  0  0  0  0  0  0  0
+ 0  0  0  0  0  0  0  0  0  0  0
+ 0  0  0  0  0  0  0  0  0  0  0
+ 0  0  0  0  0  0  0  0  0  0  0
+];
+
+# ╔═╡ 2680e980-f8f5-11ea-10c2-fbf1d8358506
+g = SimpleDiGraph(A)
+
+# ╔═╡ 53e56540-f8f5-11ea-1189-99d9421b9146
+gplot(g, nodelabel=1:nv(g))
+
+# ╔═╡ 7563a7d0-f8f6-11ea-00ae-bbee824a385c
+genetic_knowper(g, normalize=:none)
+
+# ╔═╡ 6b60e68e-f8f5-11ea-25f9-f3075e37b317
+mpres = mainpath(g, 3, GBFP(), normalize=:none)
+
+# ╔═╡ 3404b0a0-f8f5-11ea-1cb0-4f35dff35a1f
+mpnet, vlabels = induced_subgraph(g, mpres.edges)
+
+# ╔═╡ bd8334f0-f8f5-11ea-0def-dda12adf86e7
+gplot(mpnet, nodelabel=vlabels)
+
+# ╔═╡ 5bb78380-f8f9-11ea-2b66-1529d729d0d9
+function add_weights(g, w)
+    mg = MetaDiGraph(g)
+	for (i,e) in enumerate(edges(g))
+		set_prop!(mg, e, :weight, w[i])
+	end
+	return mg
+end
+
+# ╔═╡ c9fba690-f8f5-11ea-068f-7393d3245730
+begin
+	spc = weights_spc(g).edgeweights
+	mg = add_weights(g, spc)
+	mpfl = mainpath(mg, ForwardLocal())
+	mpbl = mainpath(mg, BackwardLocal())
+end
+
+# ╔═╡ Cell order:
+# ╠═0120e370-f8f5-11ea-1b65-9d29b0b5b647
+# ╠═0ba77020-f8f5-11ea-025d-61768c938c5c
+# ╠═2680e980-f8f5-11ea-10c2-fbf1d8358506
+# ╠═53e56540-f8f5-11ea-1189-99d9421b9146
+# ╠═7563a7d0-f8f6-11ea-00ae-bbee824a385c
+# ╠═6b60e68e-f8f5-11ea-25f9-f3075e37b317
+# ╠═3404b0a0-f8f5-11ea-1cb0-4f35dff35a1f
+# ╠═bd8334f0-f8f5-11ea-0def-dda12adf86e7
+# ╠═5bb78380-f8f9-11ea-2b66-1529d729d0d9
+# ╠═c9fba690-f8f5-11ea-068f-7393d3245730

test/runtests.jl

@@ -22,7 +22,7 @@ A = [
 
 g = SimpleDiGraph(A)
 
-ew_spc, vw_spc, tf_spc = compute_weights_spc(g, normalize = false)
+ew_spc, vw_spc, tf_spc = weights_spc(g, normalize = false)
 
 # MetaDiGraph