R/utils.R

In gtexr: Query the GTEx Portal API

process_linkage_disequilibrium_resp_json <- function(resp_body) {

  if (rlang::is_empty(resp_body$data)) {
    return(tibble::tibble())
  }

  resp_body$data |>
    purrr::map(\(x) tibble::tibble(variants = x[[1]], ld = x[[2]])) |>
    dplyr::bind_rows() |>
    tidyr::separate_wider_delim(
      cols = "variants",
      delim = ",",
      names = c("variantId_1", "variantId_2")
    ) |>
    dplyr::mutate("ld" = as.numeric(.data[["ld"]]))
}

process_clustered_expression_resp_json <- function(resp_json, expression_item_name) {
  if (!expression_item_name %in% names(resp_json)) {
    cli::cli_abort(
      c(
        "Internal gtexr error - incorrect `expression_item_name`: '{expression_item_name}'",
        "i" = "Please submit an issue at {.url {packageDescription('gtexr')$BugReports}} with a reproducible example."
      )
    )
  }

  result <-
    resp_json[[expression_item_name]] |>
    purrr::map(tibble::as_tibble) |>
    dplyr::bind_rows()

  attr(result, "clusters") <- resp_json$clusters

  cli::cli_alert_info("Retrieve clustering data with `attr(<df>, 'clusters')`")

  return(result)
}

n_items_exceeds_page_size_warning <- function(fn_name, n_items, maxItemsPerPage) {
  warning_message <-
    c(
      "!" = cli::format_inline(
        "Total number of items ({n_items}) exceeds the selected maximum page size ({maxItemsPerPage})."
      ),
      "x" = cli::format_inline("{n_items - maxItemsPerPage} items were not retrieved."),
      "i" = cli::format_inline(
        c("To retrieve all available items, increase `itemsPerPage`, ensuring you reuse your original query parameters",
        " e.g. `{fn_name}(<your_existing_parameters>, itemsPerPage = 100000)`")
      ),
      "i" = cli::format_inline(
        "Alternatively, adjust global \"gtexr.itemsPerPage\" setting e.g. `options(list(gtexr.itemsPerPage = 100000))`"
      )
    )

  cli::cli_warn(warning_message, message_unformatted = warning_message)
}