Plot a Multiplex Ecological Network Organized by Trophic Level using visNetwork

Extends plot_troph_level_visNet() to multiplex ecological networks, where species interact through several distinct types of interactions (e.g. trophic vs. non-trophic: facilitation, competition, commensalism, amensalism) represented as separate "layers" sharing the same set of nodes. Trophic level is computed using only the trophic layer, while all layers are drawn together with distinguishable edge colors/styles and an interactive layer filter.

Usage

plot_troph_level_visNet_multi(
  g,
  layer_attr = "layer",
  trophic_layer = "trophic",
  vertexSizeMin = 8,
  vertexSizeMax = 25,
  modules = FALSE,
  weights = NA,
  community_obj = NULL,
  node_weights = NA,
  module_spacing = 350,
  physics = c("x", "full"),
  highlight = TRUE,
  search = TRUE,
  label_size = 16,
  layer_colors = NULL,
  layer_dashed = NULL,
  layer_filter = TRUE,
  legend = TRUE,
  width = "100%",
  height = "850px"
)

Arguments

g: Either (a) a single igraph object with an edge attribute (named by layer_attr) identifying the interaction type of each edge, or (b) a named list of igraph objects, one per layer, all sharing (a subset of) the same vertex set via V(g)$name. List names are used as layer labels.
layer_attr: Name of the edge attribute holding the layer/interaction-type label, used only when g is a single igraph object (default: "layer").
trophic_layer: Value identifying which layer represents trophic (feeding) interactions; used to compute trophic level via NetIndices::TrophInd() (default: "trophic"). Species with no trophic-layer edges (e.g. species that only participate in non-trophic interactions) are assigned trophic level = 1 for display purposes, with a warning.
vertexSizeMin, vertexSizeMax: Minimum/maximum node size (defaults: 8, 25).
modules: Logical; if TRUE, nodes are grouped by community modules along the x-axis, detected on the flattened (all-layers-pooled) network (default: FALSE).
weights: Edge weights used for community detection when modules = TRUE and community_obj is not supplied (default: NA).
community_obj: Optional pre-computed community detection object.
node_weights: Optional numeric vector used to size nodes. If NA (default), total node degree pooled across all layers is used, so multiplex hubs are sized according to their combined role across interaction types.
module_spacing: Horizontal spacing multiplier between community modules (default: 350).
physics: Layout mode, "x" (default) or "full" — see plot_troph_level_visNet() for details. In both modes, physics is disabled and node positions are unlocked once stabilization finishes, so the trophic-level ordering ("x") or force-directed layout ("full") is only the starting point; afterwards any node can be freely dragged in any direction.
highlight: Logical; hover-highlight nearest neighbors (default: TRUE).
search: Logical; add node-search dropdown (default: TRUE).
label_size: Node label font size in pixels (default: 16).
layer_colors: Optional named character vector mapping layer names to edge colors. If NULL (default), a viridisLite palette is generated automatically.
layer_dashed: Optional character vector of layer names whose edges should be drawn dashed, to distinguish them from solid edges regardless of color (typically used to mark non-trophic layers, e.g. layer_dashed = c("facilitation","competition")).
layer_filter: Logical; if TRUE (default), adds an interactive dropdown to filter/isolate edges by layer.
legend: Logical; if TRUE (default), displays the layer-type legend.
width: Width of the visNetwork widget (default: "100%"). Accepts any CSS width string.
height: Height of the visNetwork widget (default: "850px"). Accepts any CSS height string. When embedding in slide frameworks like xaringan, set an explicit pixel height small enough to fit the slide (e.g. "400px") — the widget does not shrink to fit its container automatically.

Value

A visNetwork HTML widget.

Details

When present, existing igraph visual attributes are respected: vertex color and size, and edge color and width.