R/enrichr_lib_call.R

In CogDisResLab/KRSA: KRSA: Kinome Random Sampling Analyzer

#' Runs enrichr api (single GET call for a geneset library)
#'
#' This function takes in the geneset library name from Enrichr and
#' userListId (id created by enrichr api) sand retruns tidy dataframe of
#' all geneset terms in that library
#'
#' @param lib geneset library name from Enrichr
#' @param userListId id created by the POST enrichr api call
#'
#' @return df tidy dataframe of all geneset terms in that library
#'
#' @family helper functions
#'
#' @export
#'
#'
#' @examples
#' TRUE
enrichr_lib_call <- function(lib, userListId) {
    ENRICHR_URL <- "https://maayanlab.cloud/Enrichr/enrich"
    query_string <- "?userListId=%s&backgroundType=%s"


    full_link <- base::paste0(
        ENRICHR_URL,
        "?userListId=",
        userListId,
        "&backgroundType=",
        lib
    )

    base::message(base::paste0(lib, " ..."))

    res <- base::suppressMessages(jsonlite::fromJSON(httr::content(
        httr::GET(full_link),
        as = "text"
    )))

    purrr::map(res[[1]], process_output) %>%
        purrr::map_df(dplyr::bind_rows) %>%
        dplyr::mutate(lib = lib)
}

process_output <- function(x) {
    x <- stats::setNames(x, c(
        "index", "term", "pvalue", "odds_ratio", "combined_score",
        "genes", "adjusted_pvalue", "old1", "old2"
    ))

    x[["genes"]] <- base::paste0(x[["genes"]], collapse = ", ")

    x
}