R/join_phecode_info.R

In nstrayer/phewasHelper: Helpers For Working With PheWas And PheCode Data

#' Join data with phecode information
#'
#' Takes a dataframe with a phecode column in it and desired new phecode
#' information columns to it: `description`, `category`, `category_number`, and
#' `phecode_index` (the relative position in ordered phenome of phecode).
#'
#' @param data_w_phecode Dataframe with a phecode column.
#' @param phecode_column Unquoted column of passed data that contains phecodes
#' @param cols_to_join Which columns of phecode info do you want appended to
#'   dataframe?
#'
#' @return input dataframe with three columns added to it.
#'
#' @seealso get_phecode_info
#'
#' @export
#'
#' @examples
#'
#' library(dplyr)
#'
#' data_w_phecode <- sample_n(phecode_descriptions, 100) %>%
#'   select(phecode) %>%
#'   mutate(random = rnorm(n()))
#'
#' # Default values
#' data_w_phecode %>%
#'   join_phecode_info()
#'
#' # Can change name of phecode column
#' data_w_phecode %>%
#'   rename(jd_code = phecode) %>%
#'   join_phecode_info(jd_code)
#'
#' # Can choose which columns are added
#' data_w_phecode %>%
#'   join_phecode_info(cols_to_join = c("description", "phecode_index"))
#'
join_phecode_info <- function(data_w_phecode,
                              phecode_column = phecode,
                              cols_to_join = c("description", "category", "category_number", "phecode_index")){

  phecode_column_name <- rlang::quo_name(rlang::enquo(phecode_column))

  phecode_col_missing <- !(phecode_column_name %in% colnames(data_w_phecode))


  # cols_to_join = c("description", "phecode_index", "a cool col")
  if(phecode_col_missing){
    stop("Missing phecode column in data. Make sure phecode_column argument is correct.")
  }

  has_any_appended_cols <- cols_to_join %in% colnames(data_w_phecode)
  if(any(has_any_appended_cols)){
    warning("Existing info columns in input. Joined info columns will be suffixed with '_info'.")
  }

  available_info_cols <- colnames(phecode_descriptions)

  bad_requests <- available_info_cols[!(cols_to_join %in% available_info_cols)]

  if(length(bad_requests) > 0){
    stop(paste0("The request phecode information (",
                paste(bad_requests, collapse = ","),
                (if(length(bad_requests) == 1) ") is" else "are"),
                " unavailable. Possible information values include: ",
                paste(available_info_cols, collapse = ", ")))
  }

  dplyr::left_join(data_w_phecode,
                   dplyr::select(phecode_descriptions, phecode, dplyr::one_of(cols_to_join)),
                   suffix = c("", "_info"),
                   by = rlang::set_names("phecode", phecode_column_name))
}