Creating Subgraph using igraph in R

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遇见更好的自我
遇见更好的自我 2021-01-06 08:48

I need to obtain a subgraph of the seed nodes (the input list of nodes; file.txt) and their first interactors (neighbours) from a graph (g) using igraph. Unfortunately, I am

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  •  挽巷
    挽巷 (楼主)
    2021-01-06 09:07

    I'm not sure to have completely understood your problem, so I have created a (hopefully) self-explanatory example:

    # for example reproducibility
    set.seed(123)
    
    # create a fake undirected graph
    D <- read.table(
    sep=',',
    header=T,
    text=
    'from,to
    A,B
    A,C
    D,E
    F,G
    H,I')
    
    g1 <- graph.data.frame(D,directed=F)
    plot(g1)
    
    # we want a sub-network containing the floowing nodes:
    subv <- c('A','B','H')
    
    # first method: 
    # create a sub-network composed by ONLY the nodes in subv and the edges 
    # between them
    g2 <- induced.subgraph(graph=g1,vids=subv)
    plot(g2)
    
    # second method: 
    # create a sub-network composed by the nodes in subv and, if some of them is
    # connected to other nodes (even if not in subv), take also them 
    # (and of course include all the edges among this bunch of nodes). 
    sg1 <- decompose.graph(g1,mode="weak")
    neighverts <- unique(unlist(sapply(sg1,FUN=function(s){if(any(V(s)$name %in% subv)) V(s)$name else NULL})))
    g3 <- induced.subgraph(graph=g1,vids=neighverts)
    plot(g3)
    

    Graph g1 :

    g1

    Graph g2 :

    g2

    Graph g3 :

    g3

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