R/ggnetworkmap.R

In ggobi/ggally: Extension to 'ggplot2'

if (getRversion() >= "2.15.1") {
  utils::globalVariables(c(
    "lon", "lat", "group", "id",
    "lon1", "lat1", "lon2", "lat2",
    ".label"
  ))
}

#' Network plot map overlay
#'
#' Plots a network with \pkg{ggplot2} suitable for overlay on a \pkg{ggmap} plot or \pkg{ggplot2}
#'
#' This is a descendant of the original \code{ggnet} function.  \code{ggnet} added the innovation of plotting the network geographically.
#' However, \code{ggnet} needed to be the first object in the ggplot chain.  \code{ggnetworkmap} does not.  If passed a \code{ggplot} object as its first argument,
#' such as output from \code{ggmap}, \code{ggnetworkmap} will plot on top of that chart, looking for vertex attributes \code{lon} and \code{lat} as coordinates.
#' Otherwise, \code{ggnetworkmap} will generate coordinates using the Fruchterman-Reingold algorithm.
#'
#' @export
#' @param gg an object of class \code{ggplot}.
#' @param net an object of class \code{\link[network]{network}}, or any object
#' that can be coerced to this class, such as an adjacency or incidence matrix,
#' or an edge list: see \link[network]{edgeset.constructors} and
#' \link[network]{network} for details. If the object is of class
#' [igraph][igraph::igraph-package] and the
#' [intergraph][intergraph::intergraph-package] package is installed,
#' it will be used to convert the object: see
#' \code{\link[intergraph]{asNetwork}} for details.
#' @param size size of the network nodes. Defaults to 3. If the nodes are weighted, their area is proportionally scaled up to the size set by \code{size}.
#' @param alpha a level of transparency for nodes, vertices and arrows. Defaults to 0.75.
#' @param weight if present, the unquoted name of a vertex attribute in \code{data}.  Otherwise nodes are unweighted.
#' @param node.group \code{NULL}, the default, or the unquoted name of a vertex attribute that will be used to determine the color of each node.
#' @param ring.group if not \code{NULL}, the default, the unquoted name of a vertex attribute that will be used to determine the color of each node border.
#' @param node.color If \code{node.group} is null, a character string specifying a color.
#' @param node.alpha transparency of the nodes. Inherits from \code{alpha}.
#' @param segment.alpha transparency of the vertex links. Inherits from \code{alpha}
#' @param segment.color color of the vertex links. Defaults to \code{"grey"}.
#' @param segment.size size of the vertex links, as a vector of values or as a single value. Defaults to 0.25.
#' @param great.circles whether to draw edges as great circles using the \code{geosphere} package.  Defaults to \code{FALSE}
#' @param arrow.size size of the vertex arrows for directed network plotting, in centimeters. Defaults to 0.
#' @param label.nodes label nodes with their vertex names attribute. If set to \code{TRUE}, all nodes are labelled. Also accepts a vector of character strings to match with vertex names.
#' @param label.size size of the labels.  Defaults to \code{size / 2}.
#' @param ... other arguments supplied to geom_text for the node labels. Arguments pertaining to the title or other items can be achieved through \pkg{ggplot2} methods.
#' @author Amos Elberg. Original by Moritz Marbach, Francois Briatte
#' @details This is a function for plotting graphs generated by \code{network} or \code{igraph} in a more flexible and elegant manner than permitted by ggnet.  The function does not need to be the first plot in the ggplot chain, so the graph can be plotted on top of a map or other chart.  Segments can be straight lines, or plotted as great circles.  Note that the great circles feature can produce odd results with arrows and with vertices beyond the plot edges; this is a \pkg{ggplot2} limitation and cannot yet be fixed.  Nodes can have two color schemes, which are then plotted as the center and ring around the node.  The color schemes are selected by adding scale_fill_ or scale_color_ just like any other \pkg{ggplot2} plot. If there are no rings, scale_color sets the color of the nodes.  If there are rings, scale_color sets the color of the rings, and scale_fill sets the color of the centers.  Note that additional arguments in the ... are passed to geom_text for plotting labels.
#' @importFrom utils installed.packages
#' @examples
#' # small function to display plots only if it's interactive
#' p_ <- GGally::print_if_interactive
#'
#' invisible(lapply(c("ggplot2", "maps", "network", "sna"), base::library, character.only = TRUE))
#'
#' ## Example showing great circles on a simple map of the USA
#' ## http://flowingdata.com/2011/05/11/how-to-map-connections-with-great-circles/
#' \donttest{
#' airports <- read.csv("http://datasets.flowingdata.com/tuts/maparcs/airports.csv", header = TRUE)
#' rownames(airports) <- airports$iata
#'
#' # select some random flights
#' set.seed(123)
#' flights <- data.frame(
#'   origin = sample(airports[200:400, ]$iata, 200, replace = TRUE),
#'   destination = sample(airports[200:400, ]$iata, 200, replace = TRUE)
#' )
#'
#' # convert to network
#' flights <- network(flights, directed = TRUE)
#'
#' # add geographic coordinates
#' flights %v% "lat" <- airports[network.vertex.names(flights), "lat"]
#' flights %v% "lon" <- airports[network.vertex.names(flights), "long"]
#'
#' # drop isolated airports
#' delete.vertices(flights, which(degree(flights) < 2))
#'
#' # compute degree centrality
#' flights %v% "degree" <- degree(flights, gmode = "digraph")
#'
#' # add random groups
#' flights %v% "mygroup" <- sample(letters[1:4], network.size(flights), replace = TRUE)
#'
#' # create a map of the USA
#' usa <- ggplot(map_data("usa"), aes(x = long, y = lat)) +
#'   geom_polygon(aes(group = group),
#'     color = "grey65",
#'     fill = "#f9f9f9", linewidth = 0.2
#'   )
#'
#' # overlay network data to map
#' p <- ggnetworkmap(
#'   usa, flights,
#'   size = 4, great.circles = TRUE,
#'   node.group = mygroup, segment.color = "steelblue",
#'   ring.group = degree, weight = degree
#' )
#' p_(p)
#'
#' ## Exploring a community of spambots found on Twitter
#' ## Data by Amos Elberg: see ?twitter_spambots for details
#'
#' data(twitter_spambots)
#'
#' # create a world map
#' world <- fortify(map("world", plot = FALSE, fill = TRUE))
#' world <- ggplot(world, aes(x = long, y = lat)) +
#'   geom_polygon(aes(group = group),
#'     color = "grey65",
#'     fill = "#f9f9f9", linewidth = 0.2
#'   )
#'
#' # view global structure
#' p <- ggnetworkmap(world, twitter_spambots)
#' p_(p)
#'
#' # domestic distribution
#' p <- ggnetworkmap(net = twitter_spambots)
#' p_(p)
#'
#' # topology
#' p <- ggnetworkmap(net = twitter_spambots, arrow.size = 0.5)
#' p_(p)
#'
#' # compute indegree and outdegree centrality
#' twitter_spambots %v% "indegree" <- degree(twitter_spambots, cmode = "indegree")
#' twitter_spambots %v% "outdegree" <- degree(twitter_spambots, cmode = "outdegree")
#'
#' p <- ggnetworkmap(
#'   net = twitter_spambots,
#'   arrow.size = 0.5,
#'   node.group = indegree,
#'   ring.group = outdegree, size = 4
#' ) +
#'   scale_fill_continuous("Indegree", high = "red", low = "yellow") +
#'   labs(color = "Outdegree")
#' p_(p)
#'
#' # show some vertex attributes associated with each account
#' p <- ggnetworkmap(
#'   net = twitter_spambots,
#'   arrow.size = 0.5,
#'   node.group = followers,
#'   ring.group = friends,
#'   size = 4,
#'   weight = indegree,
#'   label.nodes = TRUE, vjust = -1.5
#' ) +
#'   scale_fill_continuous("Followers", high = "red", low = "yellow") +
#'   labs(color = "Friends") +
#'   scale_color_continuous(low = "lightgreen", high = "darkgreen")
#' p_(p)
#' }
#'
ggnetworkmap <- function(
    gg,
    net,
    size = 3,
    alpha = 0.75,
    weight,
    node.group,
    node.color = NULL,
    node.alpha = NULL,
    ring.group,
    segment.alpha = NULL,
    segment.color = "grey",
    great.circles = FALSE,
    segment.size = 0.25,
    arrow.size = 0,
    label.nodes = FALSE,
    label.size = size / 2,
    ...) {
  require_namespaces(c("network", "sna"))
  # sna          # node placement if there is no ggplot object in function call

  # -- conversion to network class ---------------------------------------------

  if (inherits(net, "igraph") && "intergraph" %in% rownames(installed.packages())) {
    net <- intergraph::asNetwork(net)
  } else if (inherits(net, "igraph")) {
    stop("install the 'intergraph' package to use igraph objects with ggnet")
  }

  if (!network::is.network(net)) {
    net <- try(network::network(net), silent = TRUE)
  }

  if (!network::is.network(net)) {
    stop("could not coerce net to a network object")
  }

  # -- network functions -------------------------------------------------------

  get_v <- utils::getFromNamespace("%v%", ns = "network")

  # -- network structure -------------------------------------------------------

  vattr <- network::list.vertex.attributes(net)

  is_dir <- ifelse(network::is.directed(net), "digraph", "graph")

  if (!is.numeric(arrow.size) || arrow.size < 0) {
    stop("incorrect arrow.size value")
  } else if (arrow.size > 0 && is_dir == "graph") {
    warning("network is undirected; arrow.size ignored")
    arrow.size <- 0
  }

  if (network::is.hyper(net)) {
    stop("ggnetworkmap cannot plot hyper graphs")
  }

  if (network::is.multiplex(net)) {
    stop("ggnetworkmap cannot plot multiplex graphs")
  }

  if (network::has.loops(net)) {
    warning("ggnetworkmap does not know how to handle self-loops")
  }

  # -- ... -------------------------------------------------------

  # get arguments
  labels <- label.nodes

  # alpha default
  inherit <- function(x) ifelse(is.null(x), alpha, x)

  # get sociomatrix
  m <- network::as.matrix.network.adjacency(net)

  if (missing(gg)) {
    # mapproj doesn't need to be loaded, but
    # it needs to exist for ggplot2::coord_map() to work properly
    if (!("mapproj" %in% installed.packages())) {
      require_namespaces("mapproj")
    }
    gg <- ggplot() +
      coord_map()

    plotcord <- sna::gplot.layout.fruchtermanreingold(net, list(m, layout.par = NULL))
    plotcord <- data.frame(plotcord)
    colnames(plotcord) <- c("lon", "lat")
  } else {
    plotcord <- data.frame(
      lon = as.numeric(get_v(net, "lon")),
      lat = as.numeric(get_v(net, "lat"))
    )
  }

  # Correct vertex labels
  if (!is.logical(labels)) {
    stopifnot(length(labels) == nrow(plotcord))
    plotcord$.label <- labels
  } else if ("id" %in% vattr) {
    plotcord$.label <- as.character(get_v(net, "id"))
  } else if ("vertex.names" %in% vattr) {
    plotcord$.label <- network::network.vertex.names(net)
  }

  point_aes <- list(
    x = substitute(lon),
    y = substitute(lat)
  )
  point_args <- list(
    alpha = substitute(inherit(node.alpha))
  )

  # get node groups
  if (!missing(node.group)) {
    plotcord$.ngroup <- get_v(net, as.character(substitute(node.group)))
    if (missing(ring.group)) {
      point_aes$color <- substitute(.ngroup)
    } else {
      point_aes$fill <- substitute(.ngroup)
    }
  } else if (!missing(node.color)) {
    point_args$color <- substitute(node.color)
  } else {
    point_args$color <- substitute("black")
  }

  # rings
  if (!missing(ring.group)) {
    plotcord$.rgroup <- get_v(net, as.character(substitute(ring.group)))
    point_aes$color <- substitute(.rgroup)
    point_args$pch <- substitute(21)
  }

  #
  #
  # Plot edges
  #
  #

  # get edgelist
  edges <- network::as.matrix.network.edgelist(net)
  edges <- data.frame(
    lat1 = plotcord[edges[, 1], "lat"],
    lon1 = plotcord[edges[, 1], "lon"],
    lat2 =  plotcord[edges[, 2], "lat"],
    lon2 = plotcord[edges[, 2], "lon"]
  )
  edges <- subset(na.omit(edges), (!(lat1 == lat2 & lon2 == lon2)))

  edge_args <- list(
    linewidth = substitute(segment.size),
    alpha = substitute(inherit(segment.alpha)),
    color = substitute(segment.color)
  )
  edge_aes <- list()

  # -- edge arrows -------------------------------------------------------------

  if (!missing(arrow.size) && arrow.size > 0) {
    edge_args$arrow <- substitute(arrow(
      type   = "closed",
      length = unit(arrow.size, "cm")
    ))
  }

  # -- great circles -----------------------------------------------------------

  if (great.circles) {
    # geosphere    # great circles
    require_namespaces("geosphere")

    pts <- 25 # number of intermediate points for drawing great circles
    i <- 0 # used to keep track of groups when getting intermediate points for great circles

    edges <- ddply(
      .data = edges,
      .variables = c("lat1", "lat2", "lon1", "lon2"),
      .parallel = FALSE,
      .fun = function(x) {
        p1Mat <- x[, c("lon1", "lat1")]
        colnames(p1Mat) <- NULL
        p2Mat <- x[, c("lon2", "lat2")]
        colnames(p2Mat) <- NULL
        inter <- geosphere::gcIntermediate(
          p1 = p1Mat,
          p2 = p2Mat,
          n = pts,
          addStartEnd = TRUE,
          breakAtDateLine = TRUE
        )

        if (!is.list(inter)) {
          i <<- i + 1
          inter <- data.frame(inter)
          inter$group <- i
          return(inter)
        } else {
          if (is.matrix(inter[[1]])) {
            i <<- i + 1
            ret <- data.frame(inter[[1]])
            ret$group <- i
            i <<- i + 1
            ret2 <- data.frame(inter[[2]])
            ret2$group <- i
            return(rbind(ret, ret2))
          } else {
            ret <- data.frame(lon = numeric(0), lat = numeric(0), group = numeric(0))
            for (j in 1:length(inter)) {
              i <<- i + 1
              ret1 <- data.frame(inter[[j]][[1]])
              ret1$group <- i
              i <<- i + 1
              ret2 <- data.frame(inter[[j]][[2]])
              ret2$group <- i
              ret <- rbind(ret, ret1, ret2)
            }
            return(ret)
          }
        }
      }
    )

    edge_aes$x <- substitute(lon)
    edge_aes$y <- substitute(lat)
    edge_aes$group <- substitute(group)
    edge_args$data <- substitute(edges)
    edge_args$mapping <- do.call(aes, edge_aes)
    gg <- gg + do.call(geom_path, edge_args)
  } else {
    edge_aes$x <- substitute(lon1)
    edge_aes$y <- substitute(lat1)
    edge_aes$xend <- substitute(lon2)
    edge_aes$yend <- substitute(lat2)
    edge_args$data <- substitute(edges)
    edge_args$mapping <- do.call(aes, edge_aes)
    gg <- gg + do.call(geom_segment, edge_args)
  }

  #
  #
  # Done drawing edges, time to draws nodes
  #
  #


  # custom weights: vertex attribute
  # null weighting
  sizer <- NULL
  if (missing(weight)) {
    point_args$size <- substitute(size)
  } else {
    # Setup weight-sizing
    plotcord$.weight <- get_v(net, as.character(substitute(weight)))

    # proportional scaling
    if (is.factor(plotcord$.weight)) {
      sizer <- scale_size_discrete(name = substitute(weight), range = c(size / nlevels(plotcord$weight), size))
    } else {
      sizer <- scale_size_area(name = substitute(weight), max_size = size)
    }
    point_aes$size <- substitute(.weight)
  }

  # Add points to plot

  point_args$data <- substitute(plotcord)
  point_args$mapping <- do.call(aes, point_aes)

  gg <- gg +
    do.call(geom_point, point_args)

  if (!is.null(sizer)) {
    gg <- gg +
      sizer
  }

  # -- node labels -------------------------------------------------------------

  if (isTRUE(labels)) {
    gg <- gg + geom_text(
      data = plotcord,
      aes(x = lon, y = lat, label = .label),
      size = label.size, ...
    )
  }

  gg <- gg +
    scale_x_continuous(breaks = NULL) +
    scale_y_continuous(breaks = NULL) +
    labs(color = "", fill = "", size = "", y = NULL, x = NULL) +
    theme(
      panel.background = element_blank(),
      legend.key = element_blank()
    )

  return(gg)
}