soft-constrained_layout.R

library("bootnet")
library("qgraph")

# This sets the constraint. 1 for normal behavior, higher for more constrained layouts:
constrain <- 10

# Three similar networks:
net1 <- genGGM(10, p = 0.1, propPositive = 1, nei = 2)
net2 <- genGGM(10, p = 0.1, propPositive = 1, nei = 2)
net3 <- genGGM(10, p = 0.1, propPositive = 1, nei = 2)

# In a list:
networks <- list(net1, net2, net3)

# Average them and compute a non-scaled layout:
avg_net <- Reduce("+", networks) / length(networks)

# Layout for initial:
layout_init <- qgraph(avg_net, layout = "spring", DoNotPlot=TRUE)$layout.orig

# Now plot per network:
pdf("networks.pdf")
for (i in seq_along(networks)){
  # Number of nodes:
  n <- ncol(networks[[i]])
  
  # New layout parameters:
  layout.par <- list(
    max.delta = n / constrain, 
    area = n^2.3,
    repulse.rad = n^2.8,
    layout_init = layout_init)
  
  # Plot:
  qgraph(networks[[i]], layout = "spring",
         layout.par = layout.par)
}
dev.off()