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3D Visualization of a Multiplex Ecological Network

Source: R/plot_multiplex.R
plot_multi3D.Rd

This function generates a 3D visualization of a multiplex network composed of multiple layers (e.g., trophic, mutualistic, and competitive networks) using rgl. Layers are displayed stacked along the Z-axis. Node positions are shared across layers, and nodes can be colored by module membership or functional type. An optional aggregate layer (merging all layers) can also be displayed.

Usage

plot_multi3D(
  g.list,
  layer.colors,
  as.undirected = T,
  layer.layout = "auto",
  layer.labels = "auto",
  layer.labels.cex = 2,
  edge.colors = "auto",
  edge.normalize = F,
  edge.size.scale = 1,
  node.colors = "auto",
  node.size.values = 0.5,
  node.size.scale = 1,
  node.alpha = 1,
  edge.alpha = 1,
  layer.alpha = "auto",
  layout = "fr",
  show.nodeLabels = F,
  show.aggregate = F,
  aggr.alpha = "auto",
  aggr.color = "#dadada",
  node.colors.aggr = "#dadada",
  layer.scale = 2,
  layer.shift.x = 0,
  layer.shift.y = 0,
  layer.space = 1.5,
  FOV = 30
)

Arguments

g.list

A list of igraph objects, each representing a layer of the multiplex network.

layer.colors

A vector of colors corresponding to each network layer.

as.undirected

Logical; if TRUE, converts each layer to undirected for visualization purposes (default: TRUE).

layer.layout

A layout matrix shared by all layers, or "auto" to use layoutMultiplex() (default: "auto").

layer.labels

A character vector for labeling layers. "auto" assigns "Layer 1", "Layer 2", etc. (default: "auto").

layer.labels.cex

Numeric; text size for layer labels (default: 2).

edge.colors

Edge colors (a single color or vector per layer), or "auto" to match layer color (default: "auto").

edge.normalize

Logical; if TRUE, normalizes edge weights using logarithmic scale (default: FALSE).

edge.size.scale

Numeric or vector to control edge thickness (default: 1).

node.colors

"auto" to use layer colors, or an N x L matrix for node colors per layer.

node.size.values

"auto" to size nodes by strength, or a fixed numeric value (default: 0.5).

node.size.scale

Numeric or vector to scale node size (default: 1).

node.alpha

Transparency for nodes (0–1; default: 1).

edge.alpha

Transparency for edges (0–1; default: 1).

layer.alpha

A numeric vector with layer transparency, or "auto" to set 0.5 for all layers.

layout

A character string indicating the layout method for layoutMultiplex() (default: "fr").

show.nodeLabels

Logical; if TRUE, node labels are shown (default: FALSE).

show.aggregate

Logical; if TRUE, a layer with the aggregated network is shown (default: FALSE).

aggr.alpha

Transparency for the aggregate layer (default: "auto" which is set to 0.5).

aggr.color

Color of the background layer for the aggregate network (default: "#dadada").

node.colors.aggr

Node color used in the aggregate network (default: "#dadada").

layer.scale

Scale factor for the extent of each layer (default: 2).

layer.shift.x

Horizontal X shift per layer (default: 0).

layer.shift.y

Horizontal Y shift per layer (default: 0).

layer.space

Vertical spacing between layers along Z (default: 1.5).

FOV

Field of view for the rgl perspective visualization (default: 30).

Details

Each layer is visualized as a semi-transparent plane, on which the respective network is plotted. Nodes are shared across layers and maintain consistent positions. Optionally, the aggregated network (union of all layers) can be visualized at the top. This function is designed for ecological multiplex networks and facilitates interpretation of modular structure, interaction types, or perturbation effects.

This function is adapted from the plot_multiplex3D() function in the muxViz project.

Examples

if (FALSE) { # \dontrun{
library(multiweb)
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")


# Visualize with community-colored nodes
plot_multi3D(
  g.list = g_list,
  layer.colors = RColorBrewer::brewer.pal(3, "Set2"),
  node.colors = "auto",
  node.size.scale = 0.5,
  node.size.values = "auto",
  node.colors.aggr = "#999999",
  show.aggregate = TRUE
)
} # }