inst/misc/multiModels/graphToJSON-devel.R

In trena: Fit transcriptional regulatory networks using gene expression, priors, machine learning

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# {elements: [
#    {data: {id: 'a', score:5}, position: {x: 100, y: 200}},
#    {data: {id: 'b', score:100}, position: {x: 200, y: 200}},
#    {data: {id: 'e1', source: 'a', target: 'b'}}
#    ],  // elements array
# layout: { name: 'preset'},
# style: [{selector: 'node', style: {'content': 'data(id)'}}]
# }
.graphToJSON <- function(g)
{
    x <- '{"elements": [';
    nodes <- nodes(g)
    edgeNames <- edgeNames(g)
    edges <- strsplit(edgeNames, "~")  # a list of pairs
    edgeNames <- sub("~", "->", edgeNames)
    names(edges) <- edgeNames

    noa.names <- names(nodeDataDefaults(g))
    eda.names <- names(edgeDataDefaults(g))
    nodeCount <- length(nodes)
    edgeCount <- length(edgeNames)

    for(n in 1:nodeCount){
       printf("node %4d/%4d", n, nodeCount)
       node <- nodes[n]
       x <- sprintf('%s {"data": {"id": "%s"', x, node);
       nodeAttributeCount <- length(noa.names)
       for(i in seq_len(nodeAttributeCount)){
          noa.name <- noa.names[i];
          value <-  nodeData(g, node, noa.name)[[1]]
          if(is.numeric(value))
             x <- sprintf('%s, "%s": %s', x, noa.name, value)
          else
             x <- sprintf('%s, "%s": "%s"', x, noa.name, value)
          } # for i
       x <- sprintf('%s}', x)     # close off this node data element
       if(all(c("xPos", "yPos") %in% noa.names)){
           xPos <- as.integer(nodeData(g, node, "xPos"))
           yPos <- as.integer(nodeData(g, node, "yPos"))
           x <- sprintf('%s, "position": {"x": %d, "y": %d}', x, xPos, yPos)
           } # add position element
       x <- sprintf('%s}', x)     # close off this node data element
       if(n != nodeCount)
           x <- sprintf("%s,", x)  # another node coming, add a comma
       } # for n

    for(e in seq_len(edgeCount)) {
       edgeName <- edgeNames[e]
       edge <- edges[[e]]
       sourceNode <- edge[[1]]
       targetNode <- edge[[2]]
       x <- sprintf('%s, {"data": {"id": "%s", "source": "%s", "target": "%s"', x, edgeName, sourceNode, targetNode);
       edgeAttributeCount <- length(eda.names)
       for(i in seq_len(edgeAttributeCount)){
          eda.name <- eda.names[i];
          value <-  edgeData(g, sourceNode, targetNode, eda.name)[[1]]
          if(is.numeric(value))
             x <- sprintf('%s, "%s": %s', x, eda.name, value)
          else
             x <- sprintf('%s, "%s": "%s"', x, eda.name, value)
          } # for each edgeAttribute
       x <- sprintf('%s}}', x)     # close off this edge data element
       } # for e

    x <- sprintf("%s]}", x)

    x

} # .graphToJSON
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