R/getURL.R

In sigora: Signature Overrepresentation Analysis

#' Highlight the relevant genes for a specific pathway in its pathway diagram
#'
#' This function highlights the genes involved in the present GPS for a pathway
#' of interest in its diagram. Please note that this functionality is only
#' implemented for results of Reactome or KEGG based analyses.
#'
#' @export
#' @param yy A sigora analysis result object (created by \code{sigora}).
#' @param i The rank position of the pathway of interest in summary_results.
#' @return The URL of the pathway diagram, where the relevant genes from your
#' original query list are highlighted.
#' @seealso \code{\link{sigora}}
#' @keywords functions
#' @examples
#'
#' data('kegH')
#' set.seed(seed=12345)
#' a1<-genesFromRandomPathways(kegH,3,50)
#' ## originally selected pathways:\cr
#' a1[["selectedPathways"]]
#' ## what are the genes
#' a1[["genes"]]
#' ## sigora's results with this input:\cr
#' sigoraRes <- sigora(GPSrepo =kegH, queryList = a1[["genes"]],level = 2)
#' ## Diagram for the most significant result, where the genes from our list are highlighted in red:
#' getURL(sigoraRes,1)
#'
getURL <- function(yy, i) {
  url <- ''
  repo <-
    ifelse(substr(x = yy$summary_results[i, 1], start = 1, 2) == 'R-',
           'rea',
           'keg')

  if (repo == 'rea') {
    cat(paste("assuming this is a result from Reactome ...", "\n"))
    url <-
      paste(
        "https://reactome.org/ContentService/exporter/diagram//",
        yy$summary_results[i, 1],
        ".png?flg=",
        paste(getGenes(yy, i)[, 4], sep = '',
              collapse = ','),
        sep = ''
      )
  }

  if (repo == 'keg') {
    cat(paste("assuming this is a result from KEGG ...", "\n"))
    url <- paste(
      "https://www.genome.jp/kegg-bin/show_pathway?",
      tolower(yy$summary_results[i, 1]),
      "+",
      paste(getGenes(yy, i)[, 4], sep = '', collapse = '+'),
      sep = ''
    )
  }
  url
}