R/harmonize_spectra.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

#' @title Harmonize spectra
#'
#' @description This function harmonizes spectra headers
#'
#' @param spectra Spectra object to be harmonized
#' @param metad Metadata to identify the library
#' @param mode MS ionization mode. Must contain 'pos' or 'neg'
#' @param col_ad Name of the adduct in mgf
#' @param col_ce Name of the collision energy in mgf
#' @param col_ci Name of the compound id in mgf
#' @param col_em Name of the exact mass in mgf
#' @param col_in Name of the InChI in mgf
#' @param col_io Name of the InChI without stereo in mgf
#' @param col_ik Name of the InChIKey in mgf
#' @param col_il Name of the InChIKey without stereo in mgf
#' @param col_mf Name of the molecular formula in mgf
#' @param col_na Name of the name in mgf
#' @param col_po Name of the polarity in mgf
#' @param col_sm Name of the SMILES in mgf
#' @param col_sn Name of the SMILES without stereo in mgf
#' @param col_si Name of the spectrum id in mgf
#' @param col_sp Name of the SPLASH in mgf
#' @param col_sy Name of the synonyms in mgf
#' @param col_xl Name of the xlogp in mgf
#'
#' @return The harmonized spectra
#'
#' @examples NULL
harmonize_spectra <- function(spectra,
                              metad = get("metad", envir = parent.frame()),
                              mode,
                              col_ad = get("col_ad", envir = parent.frame()),
                              col_ce = get("col_ce", envir = parent.frame()),
                              col_ci = get("col_ci", envir = parent.frame()),
                              col_em = get("col_em", envir = parent.frame()),
                              col_in = get("col_in", envir = parent.frame()),
                              col_io = get("col_io", envir = parent.frame()),
                              col_ik = get("col_ik", envir = parent.frame()),
                              col_il = get("col_il", envir = parent.frame()),
                              col_mf = get("col_mf", envir = parent.frame()),
                              col_na = get("col_na", envir = parent.frame()),
                              col_po = get("col_po", envir = parent.frame()),
                              col_sm = get("col_sm", envir = parent.frame()),
                              col_sn = get("col_sn", envir = parent.frame()),
                              col_si = get("col_si", envir = parent.frame()),
                              col_sp = get("col_sp", envir = parent.frame()),
                              col_sy = get("col_sy", envir = parent.frame()),
                              col_xl = get("col_xl", envir = parent.frame())) {
  columns <- c(
    "adduct",
    "collision_energy",
    "compound_id",
    "exactmass",
    "formula",
    "inchi",
    "inchi_no_stereo",
    "inchikey",
    "inchikey_no_stereo",
    "name",
    "smiles",
    "smiles_no_stereo",
    "spectrum_id",
    "splash",
    "synonyms",
    "xlogp"
  )
  columns_full <-
    c(
      "adduct" = col_ad,
      "collision_energy" = col_ce,
      "compound_id" = col_ci,
      "exactmass" = col_em,
      "formula" = col_mf,
      "inchi" = col_in,
      "inchi_no_stereo" = col_io,
      "inchikey" = col_ik,
      "inchikey_no_stereo" = col_il,
      "name" = col_na,
      "smiles" = col_sm,
      "smiles_no_stereo" = col_sn,
      "spectrum_id" = col_si,
      "splash" = col_sp,
      "synonyms" = col_sy,
      "xlogp" = col_xl
    )
  columns_full <- columns_full[!is.na((columns_full))]
  columns_missing <-
    columns[!columns %in% names(columns_full)]
  names(columns_missing) <- columns_missing

  spectra_missing <- columns_missing |>
    data.frame() |>
    tidytable::as_tidytable() |>
    tidytable::bind_cols(tidytable::tidytable(value = NA_character_)) |>
    tidytable::pivot_wider(names_from = columns_missing) |>
    tidytable::mutate(join = "x")

  spectra_filtered <- spectra |>
    data.frame() |>
    tidytable::as_tidytable() |>
    tidytable::filter(
      grepl(
        pattern = mode,
        x = !!as.name(col_po),
        ignore.case = TRUE
      ) | grepl(
        pattern = if (mode == "pos") {
          1
        } else {
          0
        },
        x = !!as.name(col_po),
        ignore.case = TRUE
      )
    ) |>
    tidytable::select(
      tidyselect::any_of(c(columns_full)),
      tidyselect::any_of(c("precursorCharge")),
      precursorMz,
      tidyselect::any_of(c("rtime")),
      mz,
      intensity
    ) |>
    tidytable::mutate(join = "x")

  spectra_harmonized <- spectra_filtered |>
    tidytable::full_join(spectra_missing) |>
    tidytable::select(tidyselect::any_of(c(
      "adduct",
      "collision_energy",
      "compound_id",
      "exactmass",
      "formula",
      "inchi",
      "inchi_no_stereo",
      "inchikey",
      "inchikey_no_stereo",
      "name",
      "precursorMz",
      "precursorCharge",
      "smiles",
      "smiles_no_stereo",
      "spectrum_id",
      "splash",
      "synonyms",
      "xlogp",
      "rtime",
      "mz",
      "intensity"
    ))) |>
    tidytable::mutate(
      library = metad,
      exactmass = as.numeric(exactmass),
      spectrum_id = tidytable::if_else(
        condition = is.na(spectrum_id),
        true = tidytable::row_number(),
        false = as.numeric(spectrum_id)
      ),
      compound_id = tidytable::if_else(
        condition = is.na(compound_id),
        true = name,
        false = compound_id
      )
    ) |>
    data.frame()
  rm(spectra_filtered)

  return(spectra_harmonized)
}