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

2 messages · dinesh kumar, Gábor Csárdi

dinesh kumar
# 
Dear R users

I have a similarity matrix 100X100. I used this matrix as adjacency matrix
to generate igraph graph object. Its a fully connected graph. The similarity
score is the weight of the edge. Now I want to remove all possible lowest
scores (edges) but I want to get back a fully connected graph (dont want any
isolated vertex).How can I do it?

Also is there any possibility that I can remove the edges which dont pass a
threshold (below 70% similarity score).

I attached the similarity matrix.

I would appreciate the reply

Thanks in advance

Dinesh
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.