R/wikiPathways.R

In YuLab-SMU/clusterProfiler: A universal enrichment tool for interpreting omics data

##' ORA analysis for WikiPathways
##'
##' This function performs over-representation analysis using WikiPathways
##' @title enrichWP
##' @param gene a vector of entrez gene id
##' @param organism supported organisms, which can be accessed via the get_wp_organisms() function
##' @param ... additional parameters, see also the parameters supported by the enricher() function
##' @return A \code{enrichResult} instance
##' @export
##' @author Guangchuang Yu
enrichWP <- function(gene, organism, ...) {
    wpdata <- prepare_WP_data(organism)
    res <- enricher(gene,
                    TERM2GENE = wpdata$WPID2GENE,
                    TERM2NAME = wpdata$WPID2NAME,
                    ...)
    if (is.null(res)) return(res)

    res@ontology <- "WikiPathways"
    res@organism <- organism
    res@keytype <-  "ENTREZID"

    return(res)
}


##' GSEA analysis for WikiPathways
##'
##' This function performs GSEA using WikiPathways
##' @title gseWP
##' @param geneList ranked gene list
##' @param organism supported organisms, which can be accessed via the get_wp_organisms() function
##' @param ... additional parameters, see also the parameters supported by the GSEA() function
##' @return A \code{gseaResult} instance
##' @export
##' @author Guangchuang Yu 
gseWP <- function(geneList, organism, ...) {
    wpdata <- prepare_WP_data(organism)
    res <- GSEA(geneList,
                TERM2GENE = wpdata$WPID2GENE,
                TERM2NAME = wpdata$WPID2NAME,
                ...)

    if (is.null(res)) return(res)

    res@setType <- "WikiPathways"
    res@organism <- organism
    res@keytype <-  "ENTREZID"

    return(res)
}

##' @importFrom rlang .data
prepare_WP_data <- function(organism) {
    wp2gene <- get_wp_data(organism)
    ##TERM2GENE
    wpid2gene <- wp2gene %>% dplyr::select(.data$wpid, .data$gene) 
    ##TERM2NAME
    wpid2name <- wp2gene %>% dplyr::select(.data$wpid, .data$name) 
    list(WPID2GENE = wpid2gene,
         WPID2NAME = wpid2name)
}

get_wp_gmtfile <- function() {
    wpurl <- 'https://data.wikipathways.org/current/gmt/'
    x <- yulab.utils::yread(wpurl)
    y <- x[grep('\\.gmt',x)]
    sub(".*(wikipathways-.*\\.gmt).*", "\\1",  y[grep('File', y)])
}


##' list supported organism of WikiPathways
##'
##' This function extracts information from 'https://data.wikipathways.org/current/gmt/'
##' and lists all supported organisms
##' @title get_wp_organism
##' @return supported organism list
##' @export
##' @author Guangchuang Yu
get_wp_organisms <- function() {
    gmtfile <- get_wp_gmtfile()
    orgs <- sub("wikipathways\\-\\d+\\-gmt\\-([_A-Za-z]+)\\.gmt", "\\1", gmtfile)
    sub("_", " ",  orgs)
}

##' @importFrom gson read.gmt.wp
get_wp_data <- function(organism, output = "data.frame") {
    organism <- sub(" ", "_", organism)
    gmtfile <- get_wp_gmtfile()
    wpurl <- 'https://data.wikipathways.org/current/gmt/'
    url <- paste0(wpurl,
                  gmtfile[grep(organism, gmtfile)])
    # f <- tempfile(fileext = ".gmt")
    # dl <- mydownload(url, destfile = f)
    # if (is.null(f)) {
    #     message("fail to download wikiPathways data...")
    #     return(NULL)
    # }
    # read.gmt.wp(f, output = output)

    read.gmt.wp(url, output = output)
}