R/from_cyREST.R

In KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data

#' cyREST utility functions
#' @description A subset of the R utility functions available from/defined
#'  by cyREST.  The function mapAttributes is called from within toCytoscape 
#'  which, in turn, is called from within cyto_vis. 
#' @export
#' @import methods
#' @importFrom igraph E edge_attr graph.attributes V vertex.attributes
#'  list.vertex.attributes get.edgelist ecount edge.attributes 
#'  list.edge.attributes
#' @param attr.names Attribute names of an igraph object
#' @param all.attr The attribute value if an igraph object
#' @param i The index for a given igraph object
#' @param igraphobj A graph object compatible for use with the package igraph
#' @return A JSON object to be sent to Cytoscape 


toCytoscape <- 
  function (igraphobj) {
    # Extract graph attributes
    graph_attr = graph.attributes(igraphobj)
    
    # Extract nodes
    node_count = length(V(igraphobj))
    if('name' %in% list.vertex.attributes(igraphobj)) {
      V(igraphobj)$id <- V(igraphobj)$name
    } else {
      V(igraphobj)$id <- as.character(c(1:node_count))
    }
    
    nodes <- V(igraphobj)
    v_attr = vertex.attributes(igraphobj)
    v_names = list.vertex.attributes(igraphobj)
    
    nds <- array(0, dim=c(node_count))
    for(i in 1:node_count) {
      if(i %% 1000 == 0) {
        print(i)
      }
      nds[[i]] = list(data = mapAttributes(v_names, v_attr, i))
    }
    
    edges <- get.edgelist(igraphobj)
    edge_count = ecount(igraphobj)
    e_attr <- edge.attributes(igraphobj)
    e_names = list.edge.attributes(igraphobj)
    
    attr_exists = FALSE
    e_names_len = 0
    if(identical(e_names, character(0)) == FALSE) {
      attr_exists = TRUE
      e_names_len = length(e_names)
    }
    e_names_len <- length(e_names)
    
    eds <- array(0, dim=c(edge_count))
    for(i in 1:edge_count) {
      st = list(source=toString(edges[i,1]), target=toString(edges[i,2]))
      
      # Extract attributes
      if(attr_exists) {
        eds[[i]] = list(data=c(st, mapAttributes(e_names, e_attr, i)))
      } else {
        eds[[i]] = list(data=st)
      }
      
      if(i %% 1000 == 0) {
        print(i)
      }
    }
    
    el = list(nodes=nds, edges=eds)
    
    x <- list(data = graph_attr, elements = el)
    print("Done.  To json Start...")
    return (RJSONIO::toJSON(x))
  }

#' @rdname toCytoscape
mapAttributes <-
  function(attr.names, all.attr, i) {
    attr = list()
    cur.attr.names = attr.names
    attr.names.length = length(attr.names)
    
    for(j in 1:attr.names.length) {
      if(is.na(all.attr[[j]][i]) == FALSE) {
        #       attr[j] = all.attr[[j]][i]
        attr <- c(attr, all.attr[[j]][i])
      } else {
        cur.attr.names <- cur.attr.names[cur.attr.names != attr.names[j]]
      }
    }
    names(attr) = cur.attr.names
    return (attr)
  }