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Plot an Ecological Network Organized by Trophic Level using visNetwork

Source: R/plotNetworkVis.R
plot_troph_level_visNet.Rd

This function visualizes a food web using visNetwork, where nodes represent species and edges represent interactions. Nodes are positioned by trophic level on the y-axis, and optionally, community modules on the x-axis. Unlike plot_troph_level_ggplot() and plot_troph_level_ggraph(), this produces an interactive HTML widget that supports dragging, zooming, hovering for details, and node search.

Usage

plot_troph_level_visNet(
  g,
  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,
  width = "100%",
  height = "850px"
)

Arguments

g

An igraph object representing the ecological network.

vertexSizeMin

Minimum node size (default: 8).

vertexSizeMax

Maximum node size (default: 25).

modules

Logical; if TRUE, nodes are grouped by community modules along the x-axis (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 (e.g. from cluster_spinglass()). If NULL and modules = TRUE, community detection is run internally via cluster_spinglass().

node_weights

Optional numeric vector used to size nodes. If NA (default), node degree is used.

module_spacing

Horizontal spacing multiplier between community modules when modules = TRUE (default: 350). When modules = FALSE, node x-coordinates are instead spread across a wide random range scaled by module_spacing * 1.5.

physics

Layout mode, one of "x" or "full" (default: "x").

  • "x": during the simulation, nodes can move horizontally but their vertical position stays fixed at their trophic level, so the layout settles into trophic bands.

  • "full": nodes move freely in both x and y under a force-directed layout (forceAtlas2Based), anchored by a small centralGravity to prevent unbounded drift.

In both modes, once stabilization finishes, physics is disabled and every node's fixed.x/fixed.y is unlocked, so the trophic-level ordering (in "x") or the force-directed layout (in "full") is just the starting point — afterwards any node can be freely dragged in any direction.

highlight

Logical; if TRUE, hovering over a node highlights its nearest neighbors (default: TRUE).

Logical; if TRUE, adds a node-search dropdown to the widget (default: TRUE).

label_size

Font size, in pixels, used for node labels (default: 16). Apparent label size can differ between physics modes even at the same value, since "full" typically stabilizes into a more spread-out layout that is zoomed further out to fit the view; adjust this parameter if labels look too large or too small for a given mode.

width

Width of the visNetwork widget, passed through to visNetwork::visNetwork() (default: "100%"). Accepts any CSS width string (e.g. "600px", "100%").

height

Height of the visNetwork widget, passed through to visNetwork::visNetwork() (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 visualizing the trophic structure of the network.

Examples

#
# Example using the Kefi 2015 multiplex dataset shipped with the
# 'multiweb' package (trophic + positive + negative interaction layers)
#
fileName <- system.file("extdata", package = "multiweb")
dn <- list.files(fileName, pattern = "^Kefi2015.*\\.txt$")
g <- readNetwork(dn, fileName, skipColumn = 2)
names(g) <- c("Negative", "Positive", "Trophic")

plot_troph_level_visNet_multi(g, physics = "full")
#> Warning: Can't find 'group' in node data.frame