Tutorial_day1.ipynb

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   "source": [
    "# Tutorial for running a subset of the NYC foods from Open Food Facts (https://world.openfoodfacts.org/) through Eirene.\n",
    "\n",
    "## Day 1 of 2"
   ]
  },
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   "cell_type": "markdown",
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   "source": [
    "### First we load in packages to the environment"
   ]
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      "┌ Info: Recompiling stale cache file /Users/annblevins/.julia/compiled/v1.1/Eirene/mCiG1.ji for Eirene [9c0f25c4-2ca1-5870-89f6-52640788da1d]\n",
      "└ @ Base loading.jl:1184\n",
      "┌ Warning: Package Eirene does not have Pkg in its dependencies:\n",
      "│ - If you have Eirene checked out for development and have\n",
      "│   added Pkg as a dependency but haven't updated your primary\n",
      "│   environment's manifest file, try `Pkg.resolve()`.\n",
      "│ - Otherwise you may need to report an issue with Eirene\n",
      "└ Loading Pkg into Eirene from project dependency, future warnings for Eirene are suppressed.\n"
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      "text/plain": [
       "plotBarcode (generic function with 1 method)"
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   "source": [
    "## Load packages\n",
    "\n",
    "using Pkg\n",
    "using JLD\n",
    "using Eirene\n",
    "using Combinatorics\n",
    "using SparseArrays\n",
    "using Plots\n",
    "using LightGraphs\n",
    "using GraphPlot\n",
    "\n",
    "\n",
    "function createSimplexLists(incidenceMatrix,simplex_named_list)\n",
    "    \n",
    "    # Will make lists of edges, 2-simplices, and 3-simplices\n",
    "    edge_list = Any[]\n",
    "    simp2_list = Any[]\n",
    "    simp3_list = Any[]\n",
    "    \n",
    "    for (index,simplex_name) in enumerate(simplex_named_list)\n",
    "\n",
    "        indices_of_simplex_nodes = findall(incidenceMatrix[index,:].>0)\n",
    "\n",
    "        edges_from_simplex = collect(combinations(indices_of_simplex_nodes,2))\n",
    "        simp2_from_simplex = collect(combinations(indices_of_simplex_nodes,3))\n",
    "        simp3_from_simplex = collect(combinations(indices_of_simplex_nodes,4))\n",
    "    \n",
    "\n",
    "        for (index2,edge) in enumerate(edges_from_simplex)\n",
    "            push!(edge_list,edge)\n",
    "        end\n",
    "        for (index2,simp2) in enumerate(simp2_from_simplex)\n",
    "            push!(simp2_list,simp2)\n",
    "        end\n",
    "        for (index2,simp3) in enumerate(simp3_from_simplex)\n",
    "            push!(simp3_list,simp3)\n",
    "        end\n",
    "    end\n",
    "    edge_list = unique(edge_list)\n",
    "    simp2_list = unique(simp2_list)\n",
    "    simp3_list = unique(simp3_list)\n",
    "    \n",
    "    \n",
    "    \n",
    "    return edge_list, simp2_list, simp3_list\n",
    "end\n",
    "\n",
    "\n",
    "function createCellList(nNodes,edgeList,keepTriangles)\n",
    "    n2Simps = length(keepTriangles)\n",
    "    nEdges = length(edgeList)\n",
    "    #E = Array{Array{Float64}}((Int(nNodes+nEdges+n2Simps)),1)\n",
    "    E = Array{Array{Float64,1},1}(undef,Int(nNodes+nEdges+n2Simps))\n",
    "    nCells = length(E)\n",
    "    for a0 in collect(1:nCells)\n",
    "\n",
    "        if a0 <= nNodes\n",
    "            E[a0] = [a0]\n",
    "        elseif a0 > (nNodes) && a0<=(nNodes+nEdges)\n",
    "            E[a0] = edgeList[a0-nNodes]\n",
    "        else\n",
    "            E[a0] = keepTriangles[a0-(nNodes+nEdges)]\n",
    "\n",
    "        end\n",
    "\n",
    "    end\n",
    "    E\n",
    "end\n",
    "        \n",
    "function createDMatrix(E,nNodes,nEdges)\n",
    "    D_01 = Int.(issubset.(E[1:nNodes],E[(nNodes+1):(nNodes+nEdges)]'))\n",
    "    D_12 = Int.(issubset.(E[(nNodes+1):(nNodes+nEdges)],E[(nNodes+nEdges+1):length(E)]'))\n",
    "    D = zeros(length(E),length(E))\n",
    "    D[1:nNodes,(nNodes+1):(nNodes+nEdges)] = D_01\n",
    "    D[(nNodes+1):(nNodes+nEdges),(nNodes+nEdges+1):length(E)] = D_12\n",
    "    D = sparse(D)\n",
    "end\n",
    "        \n",
    "function determineCellWeight(cell)\n",
    "    cellWeight = maximum(node_weights[Int.(cell)])\n",
    "end\n",
    "\n",
    "        \n",
    "function bettiCurveFromBarcode(barcode,nNodes,node_weights)\n",
    "\n",
    "    nNodes = Int(nNodes)\n",
    "    bettiCurve = zeros(nNodes+1,1)\n",
    "    ordered_weights = sort(unique(node_weights))\n",
    "\n",
    "    for bar in collect(1:size(barcode,1))\n",
    "        \n",
    "        birth_index = Int(findall(ordered_weights.==barcode[bar,1])[1])\n",
    "\n",
    "        if barcode[bar,2]>nNodes\n",
    "\n",
    "            bettiCurve[birth_index:Int(nNodes+1),1] = bettiCurve[birth_index:Int(nNodes+1),1] .+1\n",
    "        else\n",
    "            \n",
    "            death_index = Int(findall(ordered_weights.==barcode[bar,2])[1])\n",
    "            bettiCurve[birth_index:death_index,1] = bettiCurve[birth_index:death_index,1].+1\n",
    "                   \n",
    "        end\n",
    "    end\n",
    "\n",
    "    return bettiCurve\n",
    "end\n",
    "        \n",
    "            \n",
    "function plotBarcode(barcode,nNodes)\n",
    "\n",
    "    nNodes = Int(nNodes)\n",
    "    pbar = plot(1:6,zeros(6,1),c=:black)\n",
    "\n",
    "    barcode_sorted = barcode[sortperm(barcode[:,1]),:]\n",
    "    nbars = size(barcode)[1]\n",
    "\n",
    "\n",
    "    for bar_index in collect(1:nbars)\n",
    "        birth = barcode[bar_index,1]\n",
    "        death = barcode[bar_index,2]\n",
    "        if death>nNodes\n",
    "            death = nNodes+1\n",
    "        end\n",
    "\n",
    "        plot!([birth, death],[bar_index, bar_index],c=:blue, legend = false,\n",
    "                            xlim = (0,nNodes))\n",
    "    end\n",
    "\n",
    "\n",
    "    return pbar\n",
    "end"
   ]
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   "source": [
    "### Next load in the NYC food data. \n",
    "\n",
    "We will see a list of food products (products_list), a list of ingredients used in the food (ingredients_list), the incidence matrix indicating which ingredients are in which food products (ingredientsByProducts), and the sugar content of each product. Note for means of this tutorial any product with missing sugar information was given a value of 500."
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   "source": [
    "## Load in incidence matrix\n",
    "loaded_data = load(\"ingredientsByProducts.jld\")\n",
    "\n",
    "products_list = loaded_data[\"products_list\"]\n",
    "ingredients_list = loaded_data[\"ingredients_list\"]\n",
    "ingredientsByProducts = loaded_data[\"ingredientsByProducts\"]\n",
    "sugars = loaded_data[\"sugars\"]\n",
    "\n",
    "# Remove loaded_data to free up memory\n",
    "loaded_data = nothing\n",
    "GC.gc()\n",
    "\n",
    "\n",
    "# Quickly view the productsByIngredients incidence matrix\n",
    "gr()\n",
    "heatmap(ingredientsByProducts)\n",
    "title!(\"Producs by ingredients incidence\")\n",
    "xlabel!(\"Products\")\n",
    "ylabel!(\"Ingredients\")\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Convert incidence matrix to the proper format for Eirene\n",
    "\n",
    "Eirene can handle data in the form of an incidence matrix but requires it be converted into a simplex stream. Generally, we need to enumerate and weight each simplex within our final simplicial complex and store this in particular formats for Eirene. We will store the simplices themselves in the array of arrays E, which first has the nodes, then the edges, then the 2-simplices, and so on. Next we need to create the boundary operator D which tells us which simplices are faces of other simplices. Finally we take speciic projections of D and E (called rv, cp, and dv) together with a simplex-weight vector fv and pass these objects to eirene."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Created lists of nodes, 1-simplices, 2-simplices, and 3-simplices\n",
      "Creating cell list... \n",
      "Finished constructing cell list with 100 nodes, 535 edges, 993 2-simplices, and 1177 3-simplices.\n"
     ]
    }
   ],
   "source": [
    "## First we create lists of simplices of each dimension we care about\n",
    "\n",
    "nIngredients = size(ingredientsByProducts)[1]\n",
    "nProducts = size(ingredientsByProducts)[2]\n",
    "node_list = 1:nProducts\n",
    "\n",
    "\n",
    "edge_list, simp2_list, simp3_list = createSimplexLists(ingredientsByProducts,ingredients_list)\n",
    "# Now edge_list is an array of the edges, simp2_list an array of the 2-simplices, and so on.\n",
    "\n",
    "# Count the number of simplices we have in each dimension\n",
    "nNodes = length(node_list)\n",
    "nEdges = length(edge_list)\n",
    "nsimp2 = length(simp2_list)\n",
    "nsimp3 = length(simp3_list)\n",
    "\n",
    "println(\"Created lists of nodes, 1-simplices, 2-simplices, and 3-simplices\")\n",
    "\n",
    "\n",
    "# Combine these lists into the full cell list E\n",
    "println(\"Creating cell list... \")\n",
    "E = createCellList(nNodes,edge_list,simp2_list)\n",
    "nCells = length(E)\n",
    "\n",
    "println(\"Finished constructing cell list with $nNodes nodes, $nEdges edges, $nsimp2 2-simplices, and $nsimp3 3-simplices.\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here we compute the boundary matrix D. This matrix is composed of smaller boundary matrices that describe faces of simplices in a specific dimension. For example, the D_2 matrix of size nEdges x n2simp describes which edges make up each 2-simplex. The D_1 matrix is nNodes x nEdges and records which nodes parent each edge. The final boundary matrix D is an nCells x nCells matrix with D_1 and D_2 in the appropriate spots, and 0 elsewhere."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Constructing D matrix...\n",
      "Finished constructing boundary matrix D.\n",
      "Ready for eirene!\n"
     ]
    }
   ],
   "source": [
    "\n",
    "println(\"Constructing D matrix...\")\n",
    "D = createDMatrix(E,nNodes,nEdges)\n",
    "println(\"Finished constructing boundary matrix D.\")\n",
    "\n",
    "# D is a sparse matrix due to its size, so we can take the following \n",
    "# slices of the sparse matrix which will be enough to recover all the \n",
    "# information that eirene needs.\n",
    "rv = D.rowval\n",
    "cp = D.colptr\n",
    "dv = length.(E).-1\n",
    "\n",
    "# Assign simplex weights based on the participating food which has \n",
    "# the largest sugar content. This is where we use the node weights\n",
    "# (sugar content) to weight connections.\n",
    "\n",
    "node_weights = sugars\n",
    "fv = determineCellWeight.(E)\n",
    "\n",
    "println(\"Ready for eirene!\")\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Run Eirene! \n",
    "\n",
    "We pass our constructed objects that describe the filtration (rv,cp,dv, and fv) to eirene which returns a list C of all the persistent homology information."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Finished running persistent homology!\n"
     ]
    }
   ],
   "source": [
    "C = eirene(rv=rv,cp=cp,dv=dv,fv=fv)\n",
    "\n",
    "println(\"Finished running persistent homology!\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Vlsualize outputs\n",
    "\n",
    "### Barcodes and Betti curves\n",
    "First we wil look at the barcode output which shows each persistent cavity as a bar. Then we will plot the Betti curves, which records the number of cavities alive at each filtration value"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
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    "# Calculate Betti_1 from the barcode output\n",
    "bettiCurve_1 = bettiCurveFromBarcode(barcode(C,dim=1),nNodes,node_weights)\n",
    "\n",
    "\n",
    "# Plot!\n",
    "p1a = plot(1:(nNodes+1),bettiCurve_1, c=:blue, label = [\"B_1\"], linewidth = 2)\n",
    "xlabel!(\"Nodes added\")\n",
    "ylabel!(\"Betti_1\")\n",
    "title!(\"Betti curve\")\n",
    "p1b = plotBarcode(barcode(C,dim=1),nNodes)\n",
    "title!(\"Barcode\")\n",
    "xlabel!(\"Nodes added\")\n",
    "ylabel!(\"Persistent homology\")\n",
    "\n",
    "plot(p1a,p1b,layout = (2,1), framestyle = :box)"
   ]
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Which food to make?\n",
    "\n",
    "Now that we have discovered many cavities do indeed exist within the NYC food space, let's hone in on a few specific cavities so we can brainstorm exactly what sort of novel food combination is missing (and would be a big hit!).\n",
    "\n",
    "In this next section we'll look at specific representatives and do some food brainstorming!"
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  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
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Compose.Property{Compose.StrokePrimitive}(Compose.StrokePrimitive[StrokePrimitive(RGBA{Float64}(0.0,0.0,0.0,0.0))]), Compose.Property{Compose.FillPrimitive}(Compose.FillPrimitive[FillPrimitive(RGBA{Float64}(0.0,0.0,0.0,1.0))])]), 0, false, false, false, false, nothing, nothing, 0.0, Symbol(\"\")), Compose.Context(BBox{l,t,r,b,w,h = 0.0w,0.0h, 1.0w,1.0h, 1.0w,1.0h}, nothing, nothing, nothing, nothing, List([]), List([Compose.Form{Compose.CirclePrimitive{Tuple{Measures.Measure,Measures.Measure},Measures.Measure}}(Compose.CirclePrimitive{Tuple{Measures.Measure,Measures.Measure},Measures.Measure}[CirclePrimitive{Tuple{Measure,Measure},Measure}((-0.94488cx, -1.0cy), 0.057735w), CirclePrimitive{Tuple{Measure,Measure},Measure}((-1.0cx, 1.0cy), 0.057735w), CirclePrimitive{Tuple{Measure,Measure},Measure}((1.0cx, 0.0419174cy), 0.057735w)], Symbol(\"\"))]), List([Compose.Property{Compose.LineWidthPrimitive}(Compose.LineWidthPrimitive[LineWidthPrimitive(0.0mm)]), Compose.Property{Compose.StrokePrimitive}(Compose.StrokePrimitive[StrokePrimitive(RGBA{Float64}(0.0,0.0,0.0,0.0))]), Compose.Property{Compose.FillPrimitive}(Compose.FillPrimitive[FillPrimitive(RGBA{Float64}(0.25098,0.878431,0.815686,1.0))])]), 0, false, false, false, false, nothing, nothing, 0.0, Symbol(\"\")), Compose.Context(BBox{l,t,r,b,w,h = 0.0w,0.0h, 1.0w,1.0h, 1.0w,1.0h}, nothing, nothing, nothing, nothing, List([]), List([Compose.Form{Compose.TextPrimitive{Tuple{Measures.Length{:cx,Float64},Measures.Length{:cy,Float64}},Compose.Rotation{Tuple{Measures.Length{:w,Float64},Measures.Length{:h,Float64}}},Tuple{Measures.Length{:mm,Float64},Measures.Length{:mm,Float64}}}}(Compose.TextPrimitive{Tuple{Measures.Length{:cx,Float64},Measures.Length{:cy,Float64}},Compose.Rotation{Tuple{Measures.Length{:w,Float64},Measures.Length{:h,Float64}}},Tuple{Measures.Length{:mm,Float64},Measures.Length{:mm,Float64}}}[TextPrimitive{Tuple{Length{:cx,Float64},Length{:cy,Float64}},Rotation{Tuple{Length{:w,Float64},Length{:h,Float64}}},Tuple{Length{:mm,Float64},Length{:mm,Float64}}}((-0.94488cx, -1.0cy), \"The Original Texas Toast, Five Cheese\", HCenter(), VCenter(), Rotation{Tuple{Length{:w,Float64},Length{:h,Float64}}}(0.0, (0.5w, 0.5h)), (0.0mm, 0.0mm)), TextPrimitive{Tuple{Length{:cx,Float64},Length{:cy,Float64}},Rotation{Tuple{Length{:w,Float64},Length{:h,Float64}}},Tuple{Length{:mm,Float64},Length{:mm,Float64}}}((-1.0cx, 1.0cy), \"New York's White Pizza Sauce\", HCenter(), VCenter(), Rotation{Tuple{Length{:w,Float64},Length{:h,Float64}}}(0.0, (0.5w, 0.5h)), (0.0mm, 0.0mm)), TextPrimitive{Tuple{Length{:cx,Float64},Length{:cy,Float64}},Rotation{Tuple{Length{:w,Float64},Length{:h,Float64}}},Tuple{Length{:mm,Float64},Length{:mm,Float64}}}((1.0cx, 0.0419174cy), \"Flavored Soft Spreadable Cheese, New York Cheddar\", HCenter(), VCenter(), Rotation{Tuple{Length{:w,Float64},Length{:h,Float64}}}(0.0, (0.5w, 0.5h)), (0.0mm, 0.0mm))], Symbol(\"\"))]), List([Compose.Property{Compose.FontSizePrimitive}(Compose.FontSizePrimitive[FontSizePrimitive(4.0mm)]), Compose.Property{Compose.StrokePrimitive}(Compose.StrokePrimitive[StrokePrimitive(RGBA{Float64}(0.0,0.0,0.0,0.0))]), Compose.Property{Compose.FillPrimitive}(Compose.FillPrimitive[FillPrimitive(RGBA{Float64}(0.0,0.0,0.0,1.0))])]), 0, false, false, false, false, nothing, nothing, 0.0, Symbol(\"\"))]), List([]), List([]), 0, false, false, false, false, nothing, nothing, 0.0, Symbol(\"\"))"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The Original Texas Toast, Five Cheese\n",
      "New York's White Pizza Sauce\n",
      "Flavored Soft Spreadable Cheese, New York Cheddar\n"
     ]
    }
   ],
   "source": [
    "# Pick persistent cavity number\n",
    "class_number = 46\n",
    "\n",
    "# Extract nodes involved in the cavity and plot cycle\n",
    "rep_i = classrep(C, class = class_number, dim=1)\n",
    "nodes_in_cycle = unique(collect(Iterators.flatten(edge_list[rep_i])))\n",
    "food_in_cycle = products_list[nodes_in_cycle]\n",
    "\n",
    "g = SimpleGraph(nNodes)\n",
    "for edge in edge_list\n",
    "    add_edge!(g, edge[1], edge[2])\n",
    "end\n",
    "\n",
    "sub_graph1,vmap = induced_subgraph(g,nodes_in_cycle)\n",
    "display(gplot(sub_graph1, nodelabel = products_list[nodes_in_cycle]))\n",
    "\n",
    "for product in products_list[nodes_in_cycle]\n",
    "    println(product)\n",
    "end\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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