R/d3Network.R

In d3Network: Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R

#' Function for creating simple D3 JavaScript force directed network graphs.
#' DEPRICATED, USE d3SimpleNetwork
#'
#' \code{d3Network} creates D3 JavaScript force directed network graphs. NOTE:
#' it is depricated. It is currently a direct copy of
#' \code{\link{d3SimpleNetwork}}
#'
#' @param Data a data frame object with three columns. The first two are the
#' names of the linked units. The third records an edge value. (Currently the
#' third column doesn't affect the graph.)
#' @param Source character string naming the network source variable in the
#' data frame. If \code{Source = NULL} then the first column of the data frame
#' is treated as the source.
#' @param Target character string naming the network target variable in the
#' data frame. If \code{Target = NULL} then the second column of the data frame
#' is treated as the target.
#' @param height numeric height for the network graph's frame area in pixels.
#' @param width numeric width for the network graph's frame area in pixels.
#' @param fontsize numeric font size in pixels for the node text labels.
#' @param linkDistance numeric distance between the links in pixels (actually
#' arbitrary relative to the diagram's size).
#' @param charge numeric value indicating either the strength of the node
#' repulsion (negative value) or attraction (positive value).
#' @param linkColour character string specifying the colour you want the link
#' lines to be. Multiple formats supported (e.g. hexadecimal).
#' @param nodeColour character string specifying the colour you want the node
#' circles to be. Multiple formats supported (e.g. hexadecimal).
#' @param nodeClickColour character string specifying the colour you want the
#' node circles to be when they are clicked. Also changes the colour of the
#' text. Multiple formats supported (e.g. hexadecimal).
#' @param textColour character string specifying the colour you want the text to
#' be before they are clicked. Multiple formats supported (e.g. hexadecimal).
#' @param opacity numeric value of the proportion opaque you would like the
#' graph elements to be.
#' @param parentElement character string specifying the parent element for the
#' resulting svg network graph. This effectively allows the user to specify
#' where on the html page the graph will be placed. By default the parent
#' element is \code{body}.
#' @param standAlone logical, whether or not to return a complete HTML document
#' (with head and foot) or just the script.
#' @param file a character string of the file name to save the resulting graph.
#' If a file name is given a standalone webpage is created, i.e. with a header
#' and footer. If \code{file = NULL} then result is returned to the console.
#' @param iframe logical. If \code{iframe = TRUE} then the graph is saved to an
#' external file in the working directory and an HTML \code{iframe} linking to
#' the file is printed to the console. This is useful if you are using Slidify
#' and many other HTML slideshow framworks and want to include the graph in the
#' resulting page. If you set the knitr code chunk \code{results='asis'} then
#' the graph will be rendered in the output. Usually, you can use
#' \code{iframe = FALSE} if you are creating simple knitr Markdown or HTML
#' pages. Note: you do not need to specify the file name if
#' \code{iframe = TRUE}, however if you do, do not include the file path.
#' @param d3Script a character string that allows you to specify the location of
#' the d3.js script you would like to use. The default is
#' \url{http://d3js.org/d3.v3.min.js}.
#'
#' @source
#' D3.js was created by Michael Bostock. See \url{http://d3js.org/} and,
#' more specifically for directed networks
#' \url{https://github.com/mbostock/d3/wiki/Force-Layout}
#'
#' @importFrom whisker whisker.render
#'
#' @export

d3Network <- function(Data, Source = NULL, Target = NULL, height = 600,
    width = 900, fontsize = 7, linkDistance = 50, charge = -200,
    linkColour = "#666", nodeColour = "#3182bd", nodeClickColour = "#E34A33",
    textColour = "#3182bd", opacity = 0.6, parentElement = "body",
    standAlone = TRUE, file = NULL, iframe = FALSE,
    d3Script = "http://d3js.org/d3.v3.min.js")
{
  warning("NOTE: d3Network is depricated. Please use d3SimpleNetwork.",
        call. = FALSE)
  if (!isTRUE(standAlone) & isTRUE(iframe)){
    stop("If iframe = TRUE then standAlone must be TRUE.")
  }
  # If no file name is specified create random name to avoid conflicts
  if (is.null(file) & isTRUE(iframe)){
    Random <- paste0(sample(c(0:9, letters, LETTERS), 5, replace=TRUE),
                    collapse="")
    file <- paste0("NetworkGraph", Random, ".html")
  }

  # Create iframe dimensions larger than graph dimensions
  FrameHeight <- height + height * 0.07
  FrameWidth <- width + width * 0.03

  # Create click text size
  clickTextSize <- fontsize * 2.5

  # Subset data frame for network graph
  if (class(Data) != "data.frame"){
    stop("Data must be a data frame class object.")
  }

  if (is.null(Source) & is.null(Target)){
    NetData <- Data[, 1:2]
  }
  else if (!is.null(Source) & !is.null(Target)){
    NetData <- data.frame(Data[, Source], Data[, Target])
  }
  names(NetData) <- c("source", "target")

  # Convert data frame to JSON format
  LinkData <- toJSONarray(NetData)
  LinkData <- paste("var links =", LinkData, "; \n")

  # Create webpage head
  PageHead <- BasicHead()

  # Create Style Sheet
  NetworkCSS <- whisker.render(BasicStyleSheet())

  # Main script for creating the graph
  MainScript <- whisker.render(BasicForceJS())

  if (is.null(file) & !isTRUE(standAlone)){
    cat(NetworkCSS, LinkData, MainScript)
  }
  else if (is.null(file) & isTRUE(standAlone)){
    cat(PageHead, NetworkCSS, LinkData, MainScript,
        "</body>")
  }
  else if (!is.null(file) & !isTRUE(standAlone)){
    cat(NetworkCSS, LinkData, MainScript, file = file)
  }
  else if (!is.null(file) & !isTRUE(iframe)){
    cat(PageHead, NetworkCSS, LinkData, MainScript,
        "</body>", file = file)
  }
  else if (!is.null(file) & isTRUE(iframe)){
    cat(PageHead, NetworkCSS, LinkData, MainScript,
        "</body>", file = file)
    cat("<iframe src=\'", file, "\'", " height=", FrameHeight, " width=",
        FrameWidth, "></iframe>", sep="")
  }
}