examples-scripts/example_overlapping_generator.R

In manlius/muxViz: MuxViz - Visualization and Analysis of Multilayer Networks

library("muxViz")

#Or build by specifying layers
Layers <- 5
Nodes <- 100
NodeTensor <- list()
g.list <- list()

g.list[[1]] <- igraph::barabasi.game(Nodes, m = 1, directed = F)

#generate a second layer, with 25% edge overlap, while preserving degree distribution
g.list[[2]] <-
  GetRewiredLayerWithOverlappingEdges(g.list[[1]], 0.25, tol = 1e-2)

#generate a third layer, with 50% edge overlap, while preserving degree distribution
g.list[[3]] <-
  GetRewiredLayerWithOverlappingEdges(g.list[[1]], 0.50, tol = 1e-2)

#generate a fourth layer, with 75% edge overlap, while preserving degree distribution
g.list[[4]] <-
  GetRewiredLayerWithOverlappingEdges(g.list[[1]], 0.75, tol = 1e-2)

#generate a fifth layer, with 95% edge overlap, while preserving degree distribution
g.list[[5]] <-
  GetRewiredLayerWithOverlappingEdges(g.list[[1]], 0.95, tol = 1e-2)

#Define the layers by their adjacency matrices
for (l in 1:Layers) {
  NodeTensor[[l]] <- igraph::get.adjacency(g.list[[l]])
}

#Define how layers are interconnected
LayerTensor <- Matrix::Matrix(1, Layers, Layers) - muxViz:::speye(Layers)
#Remind that the above one is a lower-level version of this one:
#LayerTensor <- BuildLayersTensor(Layers=Layers, OmegaParameter=1, MultisliceType="Categorical")

#Build the multilayer adjacency tensor
M <-
  BuildSupraAdjacencyMatrixFromEdgeColoredMatrices(NodeTensor, LayerTensor, Layers, Nodes)

#Calculate the global edge overlap between each pair of layers
#The output numbers are arranged into a LxL matrix, encoding pairs of layers
#and should be compatible with the values imposed by construction at the beginning
OV <- GetAverageGlobalOverlappingMatrix(M, Layers, Nodes, fastBinary = T)
print(OV)

#Calculate PageRank and Degree versatility
pr <- GetMultiPageRankCentrality(M, Layers, Nodes)
deg <- GetMultiDegree(M, Layers, Nodes, isDirected = F)

mypal <- brewer.pal(Layers, "Set1")

#Generate the coordinates for layouting our networks. Using 1st layer as template.
lay <- igraph::layout_with_fr(g.list[[1]])

p <- list()

for (l in 1:length(NodeTensor)) {
  layout <- create_layout(g.list[[l]], layout = 'drl')
  layout$x <- lay[, 1]
  layout$y <- lay[, 2]

  V(g.list[[l]])$pr <- pr
  V(g.list[[l]])$deg <- deg

  p[[l]] <- ggraph(layout) + theme_void() +
    geom_edge_link(colour = mypal[l], show.legend = FALSE) +
    geom_node_point(aes(size = pr, alpha = pr), color = mypal[l]) +
    theme(
      legend.position = "bottom",
      plot.title = element_text(
        size = 16,
        hjust = 0.5,
        face = "bold",
        colour = mypal[l],
        vjust = -1
      )
    ) +
    ggtitle(paste("Layer", l)) +
    guides(size = guide_legend(title = "MuxPR"), alpha = F)
}

png(
  "mux_increasing_overlapping.png",
  width = 1024 * 1.75,
  height = 1024 * 0.5,
  res = 120
)
multiplot(p[[1]], p[[2]], p[[3]], p[[4]], p[[5]], cols = 5)
dev.off()