R/select_annotations_columns.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

#' @title Select annotations columns
#'
#' @description This function selects annotations columns
#'
#' @include columns_model.R
#' @include complement_metadata_structures.R
#' @include round_reals.R
#'
#' @param df Dataframe
#' @param str_stereo File containing structures stereo
#' @param str_met File containing structures metadata
#' @param str_nam File containing structures names
#' @param str_tax_cla File containing Classyfire taxonomy
#' @param str_tax_npc File containing NPClassifier taxonomy
#'
#' @return The dataframe with annotation columns selected
#'
#' @examples NULL
select_annotations_columns <- function(df,
                                       str_stereo = get("str_stereo", envir = parent.frame()),
                                       str_met = get("str_met", envir = parent.frame()),
                                       str_nam = get("str_nam", envir = parent.frame()),
                                       str_tax_cla = get("str_tax_cla", envir = parent.frame()),
                                       str_tax_npc = get("str_tax_npc", envir = parent.frame())) {
  model <- tima:::columns_model()
  df <- df |>
    tidytable::select(tidyselect::any_of(
      c(
        "feature_id",
        model$features_calculated_columns,
        model$candidates_calculated_columns,
        model$candidates_sirius_for_columns,
        model$candidates_sirius_str_columns,
        model$candidates_spectra_columns,
        model$candidates_structures_columns
      )
    )) |>
    tidytable::mutate(tidytable::across(
      .cols = tidyselect::where(is.character),
      .fns = function(x) {
        tidytable::na_if(x, "N/A")
      }
    )) |>
    tidytable::mutate(tidytable::across(
      .cols = tidyselect::where(is.character),
      .fns = function(x) {
        tidytable::na_if(x, "null")
      }
    )) |>
    tidytable::mutate(tidytable::across(
      .cols = tidyselect::where(is.character),
      .fns = function(x) {
        tidytable::na_if(x, "")
      }
    )) |>
    tima:::round_reals() |>
    tidytable::mutate(tidytable::across(.cols = tidyselect::where(is.numeric), .fns = as.character)) |>
    tima:::complement_metadata_structures()
  return(df)
}