R/plot.getPathviewImage.r

In BRL-BCM/MolPhenoMatch: Molecular Phenotype Patient Matchmaking

#' Retrieve the Color Coded Pathway Map based on Patient Metabolomic Profile
#'
#' @param enriched.pathwayID - The pathwayID of the pathway you want the image of.
#' @param met.profile - A character vector of a patient's metabolomic profile, including KEGG IDs
#' and the associated z-score or p-value describing the level of the metabolite compared to controls.
#' @param type - Either "p-value" or "z-score".
#' @param gene.profile - Default set to NULL, meaning the default enrichment analysis only considers metabolites.
#' However, if you have gene sets of interest, too, set this parameter to a character vector of the gene names.
#' Gene IDs must be converted to Entrez Identifiers.
#' @export plot.getPathviewImage
#' @examples
#' pathway.data = plot.getPathviewImage(met.profile)
plot.getPathviewImage = function(enriched.pathwayID, met.profile, type, gene.profile=NULL) {
  xml.file = system.file("extdata", sprintf("%s.xml", enriched.pathwayID), package="pathview")
  #node.data=node.info(xml.file)
  #plot.data.cpd=node.map(mol.data=met.profile, node.data, node.types="compound")
  #cols.ts.cpd=node.color(plot.data.cpd, limit=1, bins=10)

  #if (!is.null(gene.profile)) {
  #  path.map = node.map(mol.data=met.profile, node.data, node.types=c("gene", "compound"))
  #} else {
  #  path.map = node.map(mol.data=met.profile, node.data, node.types="compound")
  #}
  nms.perturbed.mets = names(met.profile[which(met.profile>2.5)])
  pathway.compounds = node.data$type[which(node.data$type=="compound")]
  pathCompIDs = node.data$labels[names(pathway.compounds)]

  z = met.profile[nms.perturbed.mets[which(nms.perturbed.mets %in% pathCompIDs)]]
  pathview(gene.data=NULL, cpd.data=met.profile, pathway.id=enriched.pathwayID,
           limit=list(cpd=median(z), gene=1), species="hsa", cpd.idtype="kegg")

  filename = paste(getwd(), sprintf("%s.pathview.png", enriched.pathwayID), sep="/")

  return(filename)
}