Hiii,

Can anyone tell me is there any way to find graph isomorphisam between pairs of 29 graph object together in rcytoscape ..??

I used the Protein Protein interaction data.  4539 rows and there are 29 protein which are connected to many other protein, I split the whole dataset into 29 files and now i want to find the graph isomorphism between that 29 proteins graph obbject.

please help me

Thanks.

Not sure about Cytoscape (and hence the R interface RCytoscape), but directly in R you can use the Bioconductor packages RBGL/graph or the CRAN package igraph. For example:

## using igraph package.
library(igraph)

# random graph.
g1 <- erdos.renyi.game(10, .5)
V(g1)$label <- paste("v", 1:10, sep = "-")
plot(g1)

# duplicate graph, modify labels.
g2 <- g1
V(g2)$label <- paste("f", 1:10, sep = "+")
plot(g2)

# random graph.
g3 <- erdos.renyi.game(10, .5)
plot(g3)

# check for isomorphism.
isomorphic(g1,g2) # TRUE
isomorphic(g1,g3) # FALSE
isomorphic(g2,g3) # FALSE

# obtain isomorphic mappings.
isomorphisms(g1,g2)
isomorphisms(g1,g3)

## using RBGL package.
library(RBGL)
library(graph)
library(Rgraphviz)

# random graph.
g1 <- randomEGraph(paste("v", 1:10, sep = "-"), .4)
plot(g1)

# duplicate graph, modify labels.
g2 <- g1
nodes(g2) <- paste("l", 1:10, sep = "+")
plot(g2)

# check for isomorphism.
isomorphism(g1, g2) # TRUE

# not sure if it is possible to get the isomorphic mappings...