R/createNetworkFromIgraph.R

In cytoscape/r2cytoscape: Functions for Cytoscape Automation

#' Create a Cytoscape network from an igraph network
#'
#' @description Takes an igraph network and generates data frames for nodes and edges to
#' send to the createNetwork function.
#' Returns the network.suid and applies the perferred layout set in Cytoscape preferences.
#' @details Vertices and edges from the igraph network will be translated into nodes and edges
#' in Cytoscape. Associated attributes will also be passed to Cytoscape as node and edge table columns.
#' @param igraph (igraph) igraph network object
#' @param network.name (char) network name
#' @param collection.name (char) network collection name
#' @param base.url cyrest base url for communicating with cytoscape
#' @param ... params for nodeSet2JSON() and edgeSet2JSON(); see createNetwork
#' @return (int) network SUID
#' @export
#' @import igraph
#' @examples
#' \donttest{
#' createNetworkFromIgraph(g)
#' }
#' @seealso createNetwork, createIgraphFromNetwork

createNetworkFromIgraph <- function(igraph,network.name="MyNetwork",
                          collection.name="myNetworkCollection",base.url='http://localhost:1234/v1',...) {

    #extract dataframes
    igedges = as_data_frame(igraph, what="edges")
    ignodes = as_data_frame(igraph, what="vertices")

    #setup columns for Cytoscape import
    ignodes$id <- row.names(ignodes)
    colnames(igedges)[colnames(igedges)=="from"]<-"source"
    colnames(igedges)[colnames(igedges)=="to"]<-"target"

    #ship
    createNetwork(ignodes,igedges,network.name,collection.name,base.url)
}