some little help for you, lovely bioinformatics students :)

# loading the package
require(igraph)

# some little modification on the graph merging functions
# can be found here: http://pastebin.com/hiu9dbEH
source("merge_functions.r")

# reading input files
notch <- read.graph("notch1.xml",format="graphml")
smad <- read.graph("smad2.xml",format="graphml")
axin <- read.graph("axin.xml",format="graphml")

# those graph's vertices do have `name' attribute:
# V(axin)$name
# that's required for graph.intersect.by.name()
# and graph.union.by.name() functions to work

# merge just two:
ns <- graph.union.by.name(notch,smad)
# and then the union of two with the third:
nsa <- graph.union.by.name(axin,ns)

# let's make membership matrix
# iterating on the common graph's vertices:
i <- 1
n <- a <- s <- m <- q <- NULL
for(v in V(nsa)$name){
    ifelse(length(which(V(axin)$name==v))==0,aa <- FALSE,aa <- TRUE)
    ifelse(length(which(V(smad)$name==v))==0,ss <- FALSE,ss <- TRUE)
    ifelse(length(which(V(notch)$name==v))==0,nn <- FALSE,nn <- TRUE)
    a <- c(a,aa)
    s <- c(s,ss)
    n <- c(n,nn)
}

m <- cbind(a,s,n)

# this is a little trick,
# we can do it only because we have not more than three networks
# this is how it works:
# if the node is member of the axin network, we add 1 to it's value
# if it is in the smad2 network, then we add 2
# if in case of notch1 network membership, then the increment is 4
# so all the 7 possibilities gonna be represented by an individual number
# e.g. 7 means the node is member in all the three networks
# or 6 means it's member of smad2 and notch1, but missing from the axin network
# yeah, this is the same how unix file privilege notation works, btw :)
for(v in V(nsa)$name){
    ifelse(length(which(V(axin)$name==v))==0,aa <- 0,aa <- 1)
    ifelse(length(which(V(smad)$name==v))==0,ss <- 0,ss <- 2)
    ifelse(length(which(V(notch)$name==v))==0,nn <- 0,nn <- 4)
    q <- c(q,sum(aa,ss,nn))
}

colnames(m) <- c("axin1","smad2","notch1")

# as palettes are vectors with integer indexes,
# this integer vector `q' gives an easy way to
# select different colors for the 7 groups:
rcol <- rainbow(7)
V(nsa)$color <-rcol[q]
V(nsa)$label <- V(nsa)$name
nsa$layout <- layout.kamada.kawai
E(nsa)$curved <- TRUE
cairo_pdf(filename="merged.pdf",
    onefile=TRUE,width=12,height=12,pointsize=12)
    plot(nsa)
dev.off()

# you should add some legend with the legend() function
# of course before devoff()
# please read the manual: ?legend or help(legend)
# and don't copy, please understand well every bit of R functions u use!
# denes »» [email protected] »»