R/seeker_gen_pathway.R

In Erickcufe/seekerBio: Seek gen information in databases

#' Seeker the pathway of a gen or genes
#'
#'seeker_gene_pathway is a generic function to produce a data.frame with the pathways associated with the input gen,
#'the data.frame contains the ID, name of pathway and p value. The function invokes particular methods wich depend on the class of the first argument
#'
#'
#' @param x A gen symbol
#'
#'
#' @return
#'A data.frame with the pathways of the gen from reactome.org
#'
#' @importFrom
#' jsonlite fromJSON
#'
#' @importFrom
#' purrr transpose safely
#'
#' @importFrom
#' furrr future_map
#'
#' @importFrom
#' future plan
#'
#' @author
#' Erick Cuevas Fernández
#'
#' Heriberto Manuel Rivera
#'
#' @source
#' https://reactome.org
#'
#' @examples
#'MAPT <- seeker_gen_pathway("MAPT")
#'df <- data.frame(gen=c("MAPT", "APOE", "MMP12"))
#'seeker_gen_pathway(df)
#' @rdname seeker_gen_pathway
#' @export seeker_gen_pathway
seeker_gen_pathway <- function(x) {
  UseMethod("seeker_gen_pathway")

}

#' @return \code{NULL}
#'
#' @rdname seeker_gen_pathway
#' @export
seeker_gen_pathway.character <- function(x) {

  # message(paste(Sys.time(), 'Running `seeker_gen_pathway` for character'))


  if (length(x)==1){

  server="https://reactome.org/AnalysisService/identifier/"

  informacion_Reactome <- paste(x, "/projection", sep = "", collapse = NULL)
  url_reactome <- file.path(server,informacion_Reactome, sep = "")
  datos <- jsonlite::fromJSON(url_reactome)
  paths<-datos[["pathways"]]
  paths_select <- data.frame(Gen = rep(x ,length(paths$stId)),
                             ID=paths$stId,
                              Path_name=paths$name,
                             pvalue=paths$entities$pValue)
  return(paths_select)
  } else {

    mydf <- data.frame(gene=x)
    mypaths <- seeker_gen_pathway(mydf)
    return(mypaths)
  }

}

#' @return \code{NULL}
#'
#' @rdname seeker_gen_pathway
#' @export
seeker_gen_pathway.factor <- function(x) {
  # message(paste(Sys.time(), 'Running `seeker_gen_pathway` for factor'))
  if (length(x)==1){

  server="https://reactome.org/AnalysisService/identifier/"

  informacion_Reactome <- paste(x, "/projection", sep = "", collapse = NULL)
  url_reactome <- file.path(server,informacion_Reactome, sep = "")
  datos <- jsonlite::fromJSON(url_reactome)
  paths<-datos[["pathways"]]
  paths_select <- data.frame(Gen = rep(x ,length(paths$stId)),
                             ID=paths$stId,
                             Path_name=paths$name,
                             pvalue=paths$entities$pValue)
  return(paths_select)
  } else {

    mydf <- data.frame(gene=x)
    mypaths <- seeker_gen_pathway(mydf)
    return(mypaths)
  }
}


#' @return \code{NULL}
#'
#' @rdname seeker_gen_pathway
#' @export
seeker_gen_pathway.data.frame <- function(x) {

  # message(paste(Sys.time(), 'Running `seeker_gen_pathway` for data.frame'))
  ID1 <- as.matrix(x)

  mydf <- data.frame()
  server="https://reactome.org/AnalysisService/identifier/"

  informacion_Reactome <- paste(ID1, "/projection", sep = "", collapse = NULL)
  url_reactome <- file.path(server,informacion_Reactome, sep = "")

  future::plan("multicore")

  contents <- furrr::future_map(url_reactome, purrr::safely(jsonlite::fromJSON),
                                .progress = FALSE)
  contents_1 <- purrr::transpose(contents)
  contents_request <- contents_1[["result"]]

  for (i in 1:length(contents_request)){

    paths <- contents_request[[i]][["pathways"]]

    if (length(paths)==0){
      next()
    }

    if(!is.null(paths)){

      paths_select <- data.frame(Gen = rep(ID1[i] ,length(paths$stId)),
                                 ID=paths$stId,
                                 Path_name=paths$name,
                                 pvalue=paths$entities$pValue)
      mydf <- rbind(mydf, paths_select)
    } else {
      next()
    }

  }

  mypaths <- data.frame(mydf)
  colnames(mypaths) <- c("Gen", "ID", "Path_name", "pvalue")
  return(mypaths)
}

#' @return \code{NULL}
#'
#' @rdname seeker_gen_pathway
#' @export
seeker_gen_pathway.default <- function(x) {
  stop(
    "Don't know how to make seeker_gen_pathway <",
    class(x)[[1]], ">",
    call. = FALSE
  )
}