```
# NOT RUN {
## We are not running these examples any more, because they
## take a long time (~20 seconds) to run and this is against the CRAN
## repository policy. Copy and paste them by hand to your R prompt if
## you want to run them.
# }
# NOT RUN {
# SCG of a toy network
g <- make_full_graph(5) %du% make_full_graph(5) %du% make_full_graph(5)
g <- add_edges(g, c(1,6, 1,11, 6, 11))
cg <- scg(g, 1, 3, algo="exact_scg")
#plot the result
layout <- layout_with_kk(g)
nt <- vcount(cg$Xt)
col <- rainbow(nt)
vsize <- table(cg$groups)
ewidth <- round(E(cg$Xt)$weight,2)
op <- par(mfrow=c(1,2))
plot(g, vertex.color = col[cg$groups], vertex.size = 20,
vertex.label = NA, layout = layout)
plot(cg$Xt, edge.width = ewidth, edge.label = ewidth,
vertex.color = col, vertex.size = 20*vsize/max(vsize),
vertex.label=NA, layout = layout_with_kk)
par(op)
## SCG of real-world network
library(igraphdata)
data(immuno)
summary(immuno)
n <- vcount(immuno)
interv <- c(100,100,50,25,12,6,3,2,2)
cg <- scg(immuno, ev= n-(1:9), nt=interv, mtype="laplacian",
algo="interv", epairs=TRUE)
## are the eigenvalues well-preserved?
gt <- cg$Xt
nt <- vcount(gt)
Lt <- laplacian_matrix(gt)
evalt <- eigen(Lt, only.values=TRUE)$values[nt-(1:9)]
res <- cbind(interv, cg$values, evalt)
res <- round(res,5)
colnames(res) <- c("interv","lambda_i","lambda_tilde_i")
rownames(res) <- c("N-1","N-2","N-3","N-4","N-5","N-6","N-7","N-8","N-9")
print(res)
## use SCG to get the communities
com <- scg(laplacian_matrix(immuno), ev=n-c(1,2), nt=2)$groups
col <- rainbow(max(com))
layout <- layout_nicely(immuno)
plot(immuno, layout=layout, vertex.size=3, vertex.color=col[com],
vertex.label=NA)
## display the coarse-grained graph
gt <- simplify(as.undirected(gt))
layout.cg <- layout_with_kk(gt)
com.cg <- scg(laplacian_matrix(gt), nt-c(1,2), 2)$groups
vsize <- sqrt(as.vector(table(cg$groups)))
op <- par(mfrow=c(1,2))
plot(immuno, layout=layout, vertex.size=3, vertex.color=col[com],
vertex.label=NA)
plot(gt, layout=layout.cg, vertex.size=15*vsize/max(vsize),
vertex.color=col[com.cg],vertex.label=NA)
par(op)
# }
# NOT RUN {
# }
```

Run the code above in your browser using DataLab