R/clean_collapse.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

#' @title Clean collapse
#'
#' @description This function collapses a grouped dataframe and trims it
#'
#' @param grouped_df Grouped dataframe
#' @param cols Column(s) to apply collapse to
#'
#' @return Cleaned and collapsed dataframe
#'
#' @examples NULL
clean_collapse <- function(grouped_df, cols = NULL) {
  cols <- if (is.null(cols)) {
    names(grouped_df)
  } else {
    as.character(cols)
  }

  clean_collapse_df <- grouped_df |>
    tidytable::reframe(tidytable::across(
      .cols = cols,
      .fns = function(x) {
        x <- list(paste(unique(x[!is.na(x)]), collapse = " $ "))
      }
    )) |>
    tidytable::ungroup() |>
    tidytable::mutate(tidytable::across(.cols = tidyselect::where(is.list), .fns = as.character)) |>
    tidytable::mutate(tidytable::across(.cols = tidyselect::where(is.character), .fns = trimws)) |>
    tidytable::mutate(tidytable::across(
      .cols = tidyselect::where(is.character),
      .fns = function(x) {
        tidytable::na_if(x, "")
      }
    ))

  return(clean_collapse_df)
}