R/graph.R

In jwons/provGraphR: creates adjacency matrices for lineage searches

graph.env <- new.env(parent = emptyenv())
graph.env$adj.graph <- NULL

#' creates an adjacency graph from the nodes in provParseR
#'
#' prov.parse must be called before this function
#'
#' @return nothing
#' @name create.graph
#'
#' @import provParseR
#' @import Matrix
#' @export
create.graph <- function(){

  result = tryCatch({
    get.proc.nodes()
  }, error = function(e) {
    stop("You must call prov.parse first")
  })

  # Collects all the labels of all the nodes that are put into the graph
  # Type is a vector of characters
  labels <- c(get.proc.nodes()$'label',
              get.data.nodes()$'label')

  # Collects the connections between nodes that exist in the prov
  # Originally there will be 3 columns including the labels, so
  # subset out the two columns that are required for the graph
  # Type is a matrix so that the graph can be subset by it
  edges <- as.matrix(rbind(get.proc.data()[c("entity", "activity")],
                          setNames(rev((get.data.proc()[c("activity", "entity")])),
                                   names(get.data.proc()[c("activity", "entity")])))
  )[,c("entity", "activity")]

  # Create the graph, populating each element with zeros by the length of nodes
  adj.graph <- Matrix(0, nrow = length(labels), ncol = length(labels), sparse =T)

  # Make sure the resulting matrix is labelled for grabbing the right node
  rownames(adj.graph) <- colnames(adj.graph) <- labels

  # Sets all connections to 1 by subsetting by the edges matrix
  apply(edges, 1, function(edge){
    adj.graph[edge[1], edge[2]] <<- 1
  })

  assign("adj.graph", adj.graph, envir = graph.env)

}

#' Returns lineage of provided node
#' 
#' @param node.id This is a label for a node that the lineage is
#' being requested for
#'
#' @param forward Logical that states whether or not to transpose
#' the graph allowing the function to search forward or backward
#' in lineage
#' 
#' @return a vector of characters, each will be a different node label
#' 
#' @export
#' @import igraph
#' @importFrom stats na.omit setNames
get.spine <- function(node.id, forward = F){
  
  if(!forward){
    ig <- igraph::graph_from_adjacency_matrix(graph.env$adj.graph)
  } else {
    ig <- igraph::graph_from_adjacency_matrix(t(graph.env$adj.graph))
  }

  as.character(na.omit(names(dfs(ig, node.id, "out" , unreachable = FALSE)$order)))
}