Plot Modular Structure of a Multiplex Ecological Network — plot_multiplex

This function visualizes each layer of a multiplex ecological network, with nodes colored by module membership and sized by Infomap flow values. It returns a list of ggplot objects.

Usage

plot_multiplex_modules(
  g_list,
  communities,
  module_palette = NULL,
  layout_graph = NULL,
  scale_factor = 500,
  y_by_trophic = FALSE,
  show_labels = FALSE
)

Arguments

g_list: A named list of igraph objects (e.g., from readNetwork()), each representing one layer.
communities: A data frame from run_infomap_multi()$communities, containing node, module, layer, flow.
module_palette: Optional named color palette for module IDs (default uses viridis::viridis).
layout_graph: Optional igraph object for layout (default is aggregate union of all layers).
scale_factor: Numeric multiplier for node size scaling by flow (default: 500).
y_by_trophic: Logical; if TRUE, adjusts vertical layout position using trophic level from "Trophic" layer (default: FALSE).
show_labels: Logical; if TRUE, show node names using ggrepel (default: FALSE).

Value

A named list of ggplot objects, one for each network layer.

Examples

fileName <- system.file("extdata", package = "multiweb")
dn <- list.files(fileName, pattern = "^Kefi2015.*\\.txt$")
g_list <- readNetwork(dn, fileName, skipColumn = 2)
names(g_list) <- c("Negative", "Positive", "Trophic")

res <- run_infomap_multi(g_list, layer_names = names(g_list))
plots <- plot_multiplex_modules(g_list, res$communities, y_by_trophic = TRUE)
cowplot::plot_grid(plotlist = plots, ncol = 3)
#> Warning: Removed 30 rows containing missing values or values outside the scale range
#> (`geom_point()`).
#> Warning: Removed 37 rows containing missing values or values outside the scale range
#> (`geom_point()`).