fortify.network: Fortify method for networks of class 'network'

In ggnetwork: Geometries to Plot Networks with 'ggplot2'

Fortify method for networks of class network

Description

See the vignette at https://briatte.github.io/ggnetwork/ for a description of both this function and the rest of the ggnetwork package.

Usage

## S3 method for class 'network'
fortify(
  model,
  data = NULL,
  layout = "fruchtermanreingold",
  weights = NULL,
  arrow.gap = ifelse(network::is.directed(model), 0.025, 0),
  by = NULL,
  scale = TRUE,
  stringsAsFactors = getOption("stringsAsFactors", FALSE),
  ...
)

Arguments

model	an object of class network.
data	not used by this method.
layout	a network layout supplied by gplot.layout, such as "fruchtermanreingold" (the default), or a two-column matrix with as many rows as there are nodes in the network, in which case the matrix is used as nodes coordinates.
weights	the name of an edge attribute to use as edge weights when computing the network layout, if the layout supports such weights (see 'Details'). Defaults to NULL (no edge weights).
arrow.gap	a parameter that will shorten the network edges in order to avoid overplotting edge arrows and nodes; defaults to 0 when the network is undirected (no edge shortening), or to 0.025 when the network is directed. Small values near 0.025 will generally achieve good results when the size of the nodes is reasonably small.
by	a character vector that matches an edge attribute, which will be used to generate a data frame that can be plotted with facet_wrap or facet_grid. The nodes of the network will appear in all facets, at the same coordinates. Defaults to NULL (no faceting).
scale	whether to (re)scale the layout coordinates. Defaults to TRUE, but should be set to FALSE if layout contains meaningful spatial coordinates, such as latitude and longitude.
stringsAsFactors	whether vertex and edge attributes should be converted to factors if they are of class character. Defaults to the value of getOption("stringsAsFactors"), which is FALSE by default: see data.frame.
...	additional parameters for the layout argument; see gplot.layout for available options.

Details

fortify.network will return a warning if it finds duplicated edges after converting the network to an edge list. Duplicated edges should be eliminated in favour of single weighted edges before using a network layout that supports edge weights, such as the Kamada-Kawai force-directed placement algorithm.

Value

a data.frame object.

Examples

if (require(ggplot2) && require(network)) {

  # source: ?network::flo
  data(flo)

  # data example
  ggnetwork(flo)

  # plot example
  ggplot(ggnetwork(flo), aes(x, y, xend = xend, yend = yend)) +
    geom_edges(alpha = 0.5) +
    geom_nodes(size = 12, color = "white") +
    geom_nodetext(aes(label = vertex.names), fontface = "bold") +
    theme_blank()

  # source: ?network::emon
  data(emon)

  # data example
  ggnetwork(emon[[1]], layout = "target", niter = 100)

  # data example with edge weights
  ggnetwork(emon[[1]], layout = "kamadakawai", weights = "Frequency")

  # plot example with straight edges
  ggplot(
    ggnetwork(emon[[1]], layout = "kamadakawai", arrow.gap = 0.025),
    aes(x, y, xend = xend, yend = yend)
  ) +
    geom_edges(aes(color = Frequency),
      arrow = arrow(length = unit(10, "pt"), type = "closed")
    ) +
    geom_nodes(aes(size = Formalization)) +
    scale_color_gradient(low = "grey50", high = "tomato") +
    scale_size_area(breaks = 1:3) +
    theme_blank()

  # plot example with curved edges
  ggplot(
    ggnetwork(emon[[1]], layout = "kamadakawai", arrow.gap = 0.025),
    aes(x, y, xend = xend, yend = yend)
  ) +
    geom_edges(aes(color = Frequency),
      curvature = 0.1,
      arrow = arrow(length = unit(10, "pt"), type = "open")
    ) +
    geom_nodes(aes(size = Formalization)) +
    scale_color_gradient(low = "grey50", high = "tomato") +
    scale_size_area(breaks = 1:3) +
    theme_blank()

  # facet by edge attribute
  ggplot(
    ggnetwork(emon[[1]], arrow.gap = 0.02, by = "Frequency"),
    aes(x, y, xend = xend, yend = yend)
  ) +
    geom_edges(arrow = arrow(length = unit(5, "pt"), type = "closed")) +
    geom_nodes() +
    theme_blank() +
    facet_grid(. ~ Frequency, labeller = label_both)

  # user-provided layout
  ggplot(
    ggnetwork(emon[[1]], layout = matrix(runif(28), ncol = 2)),
    aes(x, y, xend = xend, yend = yend)
  ) +
    geom_edges(arrow = arrow(length = unit(5, "pt"), type = "closed")) +
    geom_nodes() +
    theme_blank()
}

ggnetwork documentation built on May 29, 2024, 1:32 a.m.