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i graph library: how can generates a fully connected graph from a similarity matrix

Gábor Csárdi
On Fri, Dec 12, 2008 at 2:10 AM, dinesh kumar <barupal at gmail.com> wrote:
Actually your matrix is only 87x87.

If you mean that you want a graph with 87 vertices, and some edge
weights being zero, then you can simply do (assuming there are no
negative edge weights)

G <- graph.adjacency(adjmat+1, mode="undirected", weighted=TRUE)
E(G)$weight <- E(G)$weight - 1

If you mean that you want to remove isolate vertices after creating
the graph, that would be:

G <- graph.adjacency(adjmat, mode="undirected", weighted=TRUE)
G <- remove.vertices(G, V(G)[ degree(G)==0 ])

(For your data nothing really happens, there are no isolate vertices.)
You can remove it initially, from the matrix:

adjmat2 <- adjmat
adjmat2[ adjmat2 < 0.7 ] <- 0
G <- graph.adjacency(adjmat2, mode="undirected", weighted=TRUE)

or after, from the graph itself:

G <- graph.adjacency(adjmat+1, mode="undirected", weighted=TRUE)
E(G)$weight <- E(G)$weight - 1
G2 <- delete.edges(G, E(G)[ weight < 0.7 ])

Gabor

ps. there is also an igraph mailing list, you can find it from the
igraph homepage. Just in case I miss your messages here.

  
    

      
      
    

  


  


  


  
  

    

  

    
      
    
    
Thread (2 messages)

  

  

    
            
        dinesh kumar
        
        i graph library: how can generates a fully connected graph from a similarity matrix
      
      Dec 11
    
    
      
            
        Gábor Csárdi
        
        i graph library: how can generates a fully connected graph from a similarity matrix
      
      Dec 12