R/listPathways.R

In rWikiPathways: rWikiPathways - R client library for the WikiPathways API

# ------------------------------------------------------------------------------
#' @title List Pathways
#'
#' @description Retrieve list of pathways per species, including WPID, name, species,
#' URL and latest revision number.
#' @param organism (\code{character}, optional) A particular species. See \link{listOrganisms}. 
#' Default is all species.
#' @return A \code{dataframe} of pathway information
#' @examples {
#' listPathways('Mus musculus')
#' }
#' @export
#' @importFrom data.table rbindlist
listPathways <- function(organism="") {
    res <- wikipathwaysGET('listPathways', list(organism=organism))
    if(length(res$pathways) == 0){
        message("No results")
        return(data.frame())
    }
    #make into list of list (like other web service responses)
    res.pathways <- lapply(res$pathways, as.list)
    res.df <- suppressWarnings(data.table::rbindlist(res.pathways, fill = TRUE))
    res.df$revision <- vapply(res.df$revision, as.integer, integer(1)) 
    return(res.df)
}

# ------------------------------------------------------------------------------
#' @title List Pathway WPIDs
#'
#' @description Retrieve list of pathway WPIDs per species. 
#' @details Basically returns a subset of \link{listPathways} result
#' @param organism (\code{character}, optional) A particular species. See \link{listOrganisms}. 
#' Default is all species.
#' @return A \code{list} of WPIDs
#' @examples {
#' listPathwayIds('Mus musculus')
#' }
#' @seealso listPathways
#' @export 
listPathwayIds <- function(organism="") {
    res <- listPathways(organism)
    return(res$id)
}

# ------------------------------------------------------------------------------
#' @title List Pathway Names
#'
#' @description Retrieve list of pathway names per species. 
#' @details Basically returns a subset of \link{listPathways} result
#' @param organism (\code{character}, optional) A particular species. See \link{listOrganisms}. 
#' Default is all species.
#' @return A \code{list} of names
#' @examples {
#' listPathwayNames('Mus musculus')
#' }
#' @seealso listPathways
#' @export 
listPathwayNames <- function(organism="") {
    res <- listPathways(organism)
    return(res$name)
}

# ------------------------------------------------------------------------------
#' @title List Pathway URLs
#'
#' @description Retrieve list of pathway URLs per species. 
#' @details Basically returns a subset of \link{listPathways} result
#' @param organism (\code{character}, optional) A particular species. See \link{listOrganisms}. 
#' Default is all species.
#' @return A \code{list} of URLs
#' @examples {
#' listPathwayUrls('Mus musculus')
#' }
#' @seealso listPathways
#' @export 
listPathwayUrls <- function(organism="") {
    res <- listPathways(organism)
    return(res$url)
}