pause <- function() {}

### A modular graph has dense subgraphs
mod <- make_full_graph(10) %du% make_full_graph(10) %du% make_full_graph(10)
perfect <- c(rep(1, 10), rep(2, 10), rep(3, 10))
perfect

pause()

### Plot it with community (=component) colors
plot(mod, vertex.color = perfect, layout = layout_with_fr)

pause()

### Modularity of the perfect division
modularity(mod, perfect)

pause()

### Modularity of the trivial partition, quite bad
modularity(mod, rep(1, 30))

pause()

### Modularity of a good partition with two communities
modularity(mod, c(rep(1, 10), rep(2, 20)))

pause()

### A real little network, Zachary's karate club data
karate <- make_graph("Zachary")
karate$layout <- layout_with_kk(karate)

pause()

### Greedy algorithm
fc <- cluster_fast_greedy(karate)
memb <- membership(fc)
plot(karate, vertex.color = memb)

pause()

### Greedy algorithm, easier plotting
plot(fc, karate)

pause()

### Spinglass algorithm, create a hierarchical network
pref.mat <- matrix(0, 16, 16)
pref.mat[1:4, 1:4] <- pref.mat[5:8, 5:8] <-
  pref.mat[9:12, 9:12] <- pref.mat[13:16, 13:16] <- 7.5 / 127
pref.mat[pref.mat == 0] <- 5 / (3 * 128)
diag(pref.mat) <- diag(pref.mat) + 10 / 31

pause()

### Create the network with the given vertex preferences
G <- sample_pref(128 * 4, types = 16, pref.matrix = pref.mat)

pause()

### Run spinglass community detection with two gamma parameters
sc1 <- cluster_spinglass(G, spins = 4, gamma = 1.0)
sc2.2 <- cluster_spinglass(G, spins = 16, gamma = 2.2)

pause()

### Plot the adjacency matrix, use the Matrix package if available
if (require(Matrix)) {
  myimage <- function(...) image(Matrix(...))
} else {
  myimage <- image
}
A <- as_adj(G)
myimage(A)

pause()

### Ordering according to (big) communities
ord1 <- order(membership(sc1))
myimage(A[ord1, ord1])

pause()

### Ordering according to (small) communities
ord2.2 <- order(membership(sc2.2))
myimage(A[ord2.2, ord2.2])

pause()

### Consensus ordering
ord <- order(membership(sc1), membership(sc2.2))
myimage(A[ord, ord])

pause()

### Comparision of algorithms
communities <- list()

pause()

### cluster_edge_betweenness
ebc <- cluster_edge_betweenness(karate)
communities$`Edge betweenness` <- ebc

pause()

### cluster_fast_greedy
fc <- cluster_fast_greedy(karate)
communities$`Fast greedy` <- fc

pause()

### cluster_leading_eigen
lec <- cluster_leading_eigen(karate)
communities$`Leading eigenvector` <- lec

pause()

### cluster_spinglass
sc <- cluster_spinglass(karate, spins = 10)
communities$`Spinglass` <- sc

pause()

### cluster_walktrap
wt <- cluster_walktrap(karate)
communities$`Walktrap` <- wt

pause()

### cluster_label_prop
labprop <- cluster_label_prop(karate)
communities$`Label propagation` <- labprop

pause()

### Plot everything
layout(rbind(1:3, 4:6))
coords <- layout_with_kk(karate)
lapply(seq_along(communities), function(x) {
  m <- modularity(communities[[x]])
  par(mar = c(1, 1, 3, 1))
  plot(communities[[x]], karate,
    layout = coords,
    main = paste(
      names(communities)[x], "\n",
      "Modularity:", round(m, 3)
    )
  )
})

pause()

### Function to calculate clique communities
clique.community <- function(graph, k) {
  clq <- cliques(graph, min = k, max = k)
  edges <- c()
  for (i in seq(along.with = clq)) {
    for (j in seq(along.with = clq)) {
      if (length(unique(c(
        clq[[i]],
        clq[[j]]
      ))) == k + 1) {
        edges <- c(edges, c(i, j))
      }
    }
  }
  clq.graph <- simplify(graph(edges))
  V(clq.graph)$name <-
    seq(length.out = vcount(clq.graph))
  comps <- decompose(clq.graph)

  lapply(comps, function(x) {
    unique(unlist(clq[V(x)$name]))
  })
}

pause()

### Apply it to a graph, this is the example graph from
##  the original publication
g <- graph_from_literal(
  A - B:F:C:E:D, B - A:D:C:E:F:G, C - A:B:F:E:D, D - A:B:C:F:E,
  E - D:A:C:B:F:V:W:U, F - H:B:A:C:D:E, G - B:J:K:L:H,
  H - F:G:I:J:K:L, I - J:L:H, J - I:G:H:L, K - G:H:L:M,
  L - H:G:I:J:K:M, M - K:L:Q:R:S:P:O:N, N - M:Q:R:P:S:O,
  O - N:M:P, P - Q:M:N:O:S, Q - M:N:P:V:U:W:R, R - M:N:V:W:Q,
  S - N:P:M:U:W:T, T - S:V:W:U, U - E:V:Q:S:W:T,
  V - E:U:W:T:R:Q, W - U:E:V:Q:R:S:T
)

pause()

### Hand-made layout to make it look like the original in the paper
lay <- c(
  387.0763, 306.6947, 354.0305, 421.0153, 483.5344, 512.1145,
  148.6107, 392.4351, 524.6183, 541.5878, 240.6031, 20,
  65.54962, 228.0992, 61.9771, 152.1832, 334.3817, 371.8931,
  421.9084, 265.6107, 106.6336, 57.51145, 605, 20, 124.8780,
  273.6585, 160.2439, 241.9512, 132.1951, 123.6585, 343.1707,
  465.1220, 317.561, 216.3415, 226.0976, 343.1707, 306.5854,
  123.6585, 360.2439, 444.3902, 532.1951, 720, 571.2195,
  639.5122, 505.3659, 644.3902
)
lay <- matrix(lay, ncol = 2)
lay[, 2] <- max(lay[, 2]) - lay[, 2]

pause()

### Take a look at it
layout(1)
plot(g, layout = lay, vertex.label = V(g)$name)

pause()

### Calculate communities
res <- clique.community(g, k = 4)

pause()

### Paint them to different colors
colbar <- rainbow(length(res) + 1)
for (i in seq(along.with = res)) {
  V(g)[res[[i]]]$color <- colbar[i + 1]
}

pause()

### Paint the vertices in multiple communities to red
V(g)[unlist(res)[duplicated(unlist(res))]]$color <- "red"

pause()

### Plot with the new colors
plot(g, layout = lay, vertex.label = V(g)$name)