Network graph

A GPU-accelerated node-link diagram for large gene/protein interaction networks. Nodes and edges are rendered with WebGL (via sigma v3 over a graphology graph) so tens of thousands of elements stay interactive. When node coordinates are not supplied, a bounded ForceAtlas2 layout positions the nodes in the browser; otherwise the supplied x/y are used. Categorical node groups are colored from a colorblind-safe palette. Hovering a node highlights it and its neighbors; zoom and pan use sigma's camera. In a Shiny app, clicking a node sets input$<id>_selected to the clicked node id, and clicking the empty canvas clears it.

Usage

network(
  nodes,
  edges,
  layout = c("forceatlas2", "precomputed"),
  iterations = 200,
  default_node_color = "#7c8598",
  default_edge_color = "#d6dae1",
  label_threshold = 8,
  default_node_size = 4,
  directed = FALSE,
  palette = NULL,
  theme = NULL,
  width = NULL,
  height = NULL,
  element_id = NULL
)

Arguments

nodes

A data frame of nodes. Must contain an id column (coerced to character). Optional columns: x, y (precomputed coordinates), size (node radius in px), group (categorical, mapped to a palette color) and label (display name; defaults to id).

edges

A data frame of edges with columns source and target holding node ids, an optional numeric weight column (mapped to edge width), and an optional color column giving a per-edge color (else default_edge_color).

layout

Either "forceatlas2" (run a layout when coordinates are missing) or "precomputed" (require and use x/y from nodes).

iterations

Number of ForceAtlas2 iterations (bounded internally).

default_node_color

Fallback node color for nodes without a group.

default_edge_color

Edge color.

label_threshold

Minimum node size (px) for its label to render.

default_node_size

Node radius (px) used when size is absent.

directed

Draw the graph as directed, with arrowheads. When TRUE, A -> B and B -> A are kept as distinct edges; when FALSE (the default) the graph is undirected and a reciprocal pair collapses to one line.

palette

Optional character vector of hex colors overriding the default categorical palette used for node groups.

theme

Optional named list of theme overrides (colors, fonts, ...) merged over the component defaults in the browser. NULL uses the default theme.

width, height

Widget dimensions (any valid CSS size).

element_id

Optional explicit DOM id.

Value

An htmlwidget object.

Examples

set.seed(1)
nodes <- data.frame(
  id = paste0("N", 1:60),
  group = sample(c("A", "B", "C"), 60, replace = TRUE)
)
edges <- data.frame(
  source = paste0("N", sample(1:60, 120, replace = TRUE)),
  target = paste0("N", sample(1:60, 120, replace = TRUE))
)
network(nodes, edges)