Plot a dgraph with Reusable Coordinates — plot.dgraph • dgraphs

Draw each undirected edge once and color vertices by values or explicit colors. Coordinates are computed by graph.embedding() only when absent. Layout computation remains available separately in two or three dimensions.

Usage

# S3 method for class 'dgraph'
plot(
  x,
  coordinates = NULL,
  vertex.values = NULL,
  vertex.colors = NULL,
  vertex.size = 1,
  edge.alpha = 0.2,
  color.palette = NULL,
  main = "",
  add.legend = TRUE,
  stage = "final",
  method = c("fr", "kk"),
  edge.attribute = NULL,
  transform = c("identity", "reciprocal"),
  projection = NULL,
  ...
)

Arguments

x: A dgraph.
coordinates: Optional finite numeric matrix with one row per vertex and two or three columns. Row order must match graph vertex order.
vertex.values: Optional finite numeric value per vertex, mapped through color.palette. Constant values use the palette midpoint and one legend key.
vertex.colors: Optional explicit color or vector of colors, one per vertex. Cannot accompany vertex.values. Defaults to "steelblue".
vertex.size: Nonnegative point size, one value or one per vertex.
edge.alpha: Edge opacity between zero and one.
color.palette: Color vector for numeric values; defaults to a blue-white-red palette. Requires vertex.values when explicitly supplied.
main: Plot title.
add.legend: Logical; show value/color keys for numeric vertex.values. Explicit colors have no automatically inferred numeric legend.
stage: Stored graph stage, used for both layout and drawn edges.
method: Layout method, "fr" or "kk", when coordinates are absent.
edge.attribute, transform: Explicit layout edge quantity and transform; see graph.embedding(). Layout arguments cannot accompany coordinates.
projection: For three-column coordinates, two distinct column indices to display, for example c(1, 3). Three-dimensional input requires explicit projection; it is never silently flattened. Not used for two-column input.
...: Named arguments to graphics::plot.default(), such as xlim, ylim, axes, xlab, ylab, or asp. The arguments x, y and type are controlled by this method and cannot be overridden.

Value

Invisibly returns the two-column coordinates actually drawn. These can be supplied to subsequent calls to reuse the layout. Graphics settings are restored after plotting.

Examples

graph <- create.graph("cycle", n = 6)
xy <- plot(graph, vertex.values = 1:6)

plot(graph, coordinates = xy, vertex.values = rep(1, 6))

xyz <- graph.embedding(graph, dim = 3)
plot(graph, coordinates = xyz, projection = c(1, 3), vertex.colors = "navy")