R/saveAsGEXF.R

In jhilaire/guidr: This package is a wrapper to the GUIDE algorithm for decision-tree methods (Loh 2002)

# Converts the given igraph object to GEXF format and saves it at the given filepath location
#     g: input igraph object to be converted to gexf format
#     filepath: file location where the output gexf file should be saved
#
saveAsGEXF = function(g, filepath="converted_graph.gexf")
{
  require(igraph)
  require(rgexf)

  # gexf nodes require two column data frame (id, label)
  # check if the input vertices has label already present
  # if not, just have the ids themselves as the label
  if(is.null(V(g)$label))
    V(g)$label <- as.character(V(g))

  # similarily if edges does not have weight, add default 1 weight
  if(is.null(E(g)$weight))
    E(g)$weight <- rep.int(1, ecount(g))

  nodes <- data.frame(cbind(V(g), V(g)$label))
  edges <- t(Vectorize(get.edge, vectorize.args='id')(g, 1:ecount(g)))

  # combine all node attributes into a matrix (and take care of & for xml)
  vAttrNames <- setdiff(list.vertex.attributes(g), "label")
  nodesAtt <- data.frame(sapply(vAttrNames, function(attr) sub("&", "&",get.vertex.attribute(g, attr))))

  # combine all edge attributes into a matrix (and take care of & for xml)
  eAttrNames <- setdiff(list.edge.attributes(g), "weight")
  edgesAtt <- data.frame(sapply(eAttrNames, function(attr) sub("&", "&",get.edge.attribute(g, attr))))

  # combine all graph attributes into a meta-data
  graphAtt <- sapply(list.graph.attributes(g), function(attr) sub("&", "&",get.graph.attribute(g, attr)))

  # generate the gexf object
  output <- write.gexf(nodes, edges,
                       edgesWeight=E(g)$weight,
                       edgesAtt = edgesAtt,
                       nodesAtt = nodesAtt,
                       meta=c(list(creator="Gopalakrishna Palem", description="igraph -> gexf converted file", keywords="igraph, gexf, R, rgexf"), graphAtt))

  print(output, filepath, replace=T)
}