Re: [igraph] Turn a directed network into a weighted undirected network

[MikeS]

Hello,
my current code is below.
Could someone please test the code? And give comments how to optimize
it. Can I use some build-in function of igraph?


 library(igraph)
    set.seed(42)

    par(mfrow=c(1,2))

    d <- matrix(c(0,1,0,1,0, 0,0,1,1,1, 1,1,0,0,1,
0,1,1,0,1,1,1,1,0,0),nrow=5,ncol=5)

    G <- graph.adjacency(d)
    V(G)$name <- letters[1:dim(d)[1]]
    V(G)$shape = "none"
    g_layout <- layout.davidson.harel(G)
    plot(G, edge.arrow.size=0.5, edge.curved=FALSE, layout=g_layout)

    # Here are the adjacency matrices for each of the four subgraphs

    d0<-matrix(c(0,1,0,0,0,1,1,0,0),nrow=3,ncol=3)
    d1<-matrix(c(0,1,0,0,0,1,1,1,0),nrow=3,ncol=3)
    d2<-matrix(c(0,1,0,1,0,1,1,1,0),nrow=3,ncol=3)
    d3<-matrix(c(0,1,1,1,0,1,1,1,0),nrow=3,ncol=3)

    # Turn them into a convenient list
    sbgCycle.mat<-list(d0,d1,d2,d3)
    n <- length(list(d0,d1,d2,d3))

    # And then into a list of graph objects

    pattern <- lapply(sbgCycle.mat, graph.adjacency)

    # 1. Convert the directed graph to undirected one

    UG <- simplify(G)
    UG <- as.undirected(UG)

    # 2. Search for triangles in the undirected graph

    triangle <- graph.full(3)

    # names of incident vertices of triangle in the undirected graph
    sbg.triangle <- unique(graph.get.subisomorphisms.vf2(UG, triangle))
    k <- length(sbg.triangle)

    vertices_of_triangle <- function (x) { c(x[1], x[2], x[2], x[3],
x[3], x[1]) }

    vlist <- lapply(1:k, function(y) vertices_of_triangle(sbg.triangle[[y]]) )


    # 3. Search for subisomorphisms in the directed graph to all of
the four templates

    subisom1 <- subgraph_isomorphisms(pattern[[1]], G, method="lad",
induced=TRUE)
    subisom2 <- subgraph_isomorphisms(pattern[[2]], G, method="lad",
induced=TRUE)
    subisom3 <- subgraph_isomorphisms(pattern[[3]], G, method="lad",
induced=TRUE)
    subisom4 <- subgraph_isomorphisms(pattern[[4]], G, method="lad",
induced=TRUE)

    # 4. For each triangle check which pattern it was isomorphic

    vertices_of_cycle <- function(x) { c(x[1], x[2], x[3], x[1]) }

    if (length(subisom1)>0){
    for(j in 1:length(subisom1) ) {
        cycle <- as.vector(vertices_of_cycle(subisom1[[j]]))
          E(UG, path = cycle)$weight <- 1
    } # for_j
    }

    if (length(subisom2)>0){
    for(j in 1:length(subisom2) ) {
        cycle <- as.vector(vertices_of_cycle(subisom2[[j]]))
          E(UG, path = cycle)$weight <- 2
    } # for_j
    }

    if (length(subisom3)>0){
    for(j in 1:length(subisom3) ) {
        cycle <- as.vector(vertices_of_cycle(subisom3[[j]]))
          E(UG, path = cycle)$weight <- 3
    } # for_j
    }

    if (length(subisom4)>0){
    for(j in 1:length(subisom4) ) {
        cycle <- as.vector(vertices_of_cycle(subisom4[[j]]))
          E(UG, path = cycle)$weight <- 4
    } # for_j
    }

    plot(UG, edge.arrow.size=0.2, edge.label=E(UG)$weight, layout=g_layout)

--
MikeS