extract a connected subgraph from a subset of vertices with igraph

问题

I have a graph G(V,E) unweighted, undirected and connected graph with 12744 nodes and 166262 edges. I have a set of nodes (sub_set) that is a subset of V. I am interested in extracting the smallest connected subgraph where sub_set is a part of this new graph. I have managed to get a subgraph where my subset of nodes is included but I would like to know if there is a way to minimise the graph.

Here is my code (adapted from http://sidderb.wordpress.com/2013/07/16/irefr-ppi-data-access-from-r/)

library('igraph')
g <- erdos.renyi.game(10000, 0.003) #graph for illustrating my propose
sub_set <- sample(V(g), 80)
order <- 1 
edges <- get.edges(g, 1:(ecount(g)))
neighbours.vid <- unique(unlist(neighborhood(g, order, which(V(g) %in% sub_set))))
rel.vid <- edges[intersect(which(edges[,1] %in% neighbours.vid), which(edges[,2] %in%    neighbours.vid)),]
rel <- as.data.frame(cbind(V(g)[rel.vid[,1]], V(g)[rel.vid[,2]]), stringsAsFactors=FALSE)
names(rel) <- c("from", "to")
subgraph <- graph.data.frame(rel, directed=F)
subgraph <- simplify(subgraph)

I have read this post

minimum connected subgraph containing a given set of nodes, so I guess that my problem could be "The Steiner Tree problem", is there any way to try to find a suboptimal solution using igraph?

回答1:

Not sure if that's what you meant but

subgraph<-minimum.spanning.tree(subgraph)

produces a graph with the minimum number of edges in which all nodes stay connected in one component.

来源：https://stackoverflow.com/questions/23367765/extract-a-connected-subgraph-from-a-subset-of-vertices-with-igraph

标签

igraph