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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "../man/figures/"
)

library(muxViz)
library(igraph)
library(RColorBrewer)
library(ggraph)

set.seed(1)
# Network setup
Layers <- 3
Nodes <- 20
layerCouplingStrength <- 1
networkOfLayersType <- "categorical"
layer.colors <- brewer.pal(8, "Set2")

Setup fanmod, see setup fanmod vignette

pathFanmod <- "../src-exe/fanmod_linux"

Multilayer motifs

Generate an edge-colored network

nodeTensor <- list()
g.list <- list()
for (l in 1:Layers) {
  # Generate the layers
  g.list[[l]] <-
    igraph::erdos.renyi.game(Nodes, runif(1, 1.5, 2) * log(Nodes) / Nodes,
                             directed = F)

  # Get the list of adjacency matrices which build the multiplex
  nodeTensor[[l]] <- igraph::get.adjacency(g.list[[l]])
}

motifsTable <- GetMultilayerMotifsFromNetworkList(
  g.list,
  bin.path = pathFanmod,
  motifSize = 3,
  motifSamples = 100000,
  isDirected = FALSE,
  motifNullModel = "Local const",
  randomNetworks = 1000,
  randomExchangePerEdges =
    3,
  randomExchangeAttempts =
    3
)

Process the results

cutAbsZscore <- 3
cutPvalue <- 1e-3
cutFrequency <- 0.01
sortMotifsBy <- "Frequency"

sorting

print("Sorting results from motifs analysis...")
if (sortMotifsBy == "Frequency") {
  motifsTable <- motifsTable[order(-motifsTable$Frequency), ]
} else if (sortMotifsBy == "Z-score") {
  motifsTable <- motifsTable[order(-motifsTable$Z.Score), ]
} else if (sortMotifsBy == "p-value") {
  motifsTable <- motifsTable[order(motifsTable$p.Value), ]
}

cutting

print("Applying cuts to motifs table...")
motifsTable.cut <- motifsTable
motifsTable.cut <-
  motifsTable.cut[abs(motifsTable.cut$Z.Score) > cutAbsZscore,]
motifsTable.cut <-
  motifsTable.cut[motifsTable.cut$p.Value < cutPvalue,]
motifsTable.cut <-
  motifsTable.cut[motifsTable.cut$Frequency > cutFrequency,]

Plots

png("../man/figures/multi_er.png", width = 1024, height = 728 / 2,
    res = 100)
plot_multiplex(g.list, layer.colors = layer.colors, show.legend = F)
dev.off()
png("../man/figures/multi_er_fanmod.png", width = 1024, height = 728 / 2,
    res = 100)
plot_multimotif(
  motifsTable,
  motifID = 1,
  layer.colors,
  edge.colors = "auto",
  node.colors = "auto",
  node.size = 5
)
dev.off()

knitr::include_graphics("../man/figures/multi_er.png")
knitr::include_graphics("../man/figures/multi_er_fanmod.png")

manlius/muxViz documentation built on March 1, 2023, 10:28 a.m.