benchmark update

DESCRIPTION

@@ -129,7 +129,6 @@ Collate:
     'prepare_params.R'
     'prepare_taxa.R'
     'replace_id.R'
-    'sanitize_spectra_benchmark.R'
     'select_sop_columns.R'
     'taxize_spectra_benchmark.R'
     'weight_chemo.R'

NAMESPACE

@@ -61,7 +61,6 @@ export(remove_above_precursor)
 export(replace_id)
 export(round_reals)
 export(sanitize_spectra)
-export(sanitize_spectra_benchmark)
 export(select_annotations_columns)
 export(select_sirius_columns)
 export(select_sirius_columns_2)

inst/pipelines/_targets.R

@@ -1867,9 +1867,175 @@ list(
           Spectra::Spectra(source = MsBackendMsp::MsBackendMsp()) |>
           Spectra::setBackend(Spectra::MsBackendMemory())
 
-        sp |> sanitize_spectra_benchmark(
-          mgf_pos_path = benchmark_path_mgf_pos,
-          mgf_neg_path = benchmark_path_mgf_neg
+        sp$precursorMz <- as.numeric(sp$PRECURSOR_MZ)
+        sp$precursorCharge <- as.integer(sp$CHARGE)
+
+        sp_clean <- sp |>
+          Spectra::addProcessing(remove_above_precursor(),
+            spectraVariables = c("precursorMz")
+          ) |>
+          Spectra::addProcessing(normalize_peaks()) |>
+          Spectra::applyProcessing()
+
+        adduct <- sp_clean$ADDUCT
+        inchikey <- sp_clean$inchikey
+        instrument <- sp_clean$SOURCE_INSTRUMENT
+        # fragments <- sp_clean$NUM.PEAKS
+        fragments <- lapply(sp_clean@backend@peaksData, length) |>
+          as.character() |>
+          as.numeric() / 2
+        # pepmass <- gsub("\\[|\\]", "", sp_clean$PARENT_MASS)
+        pepmass <- sp_clean$PEPMASS
+        smiles <- sp_clean$smiles
+        ccmslib <- sp_clean$SPECTRUMID
+        charge <- sp_clean$precursorCharge
+
+        df_meta <- tidytable::tidytable(
+          adduct,
+          inchikey,
+          instrument,
+          fragments,
+          pepmass,
+          smiles,
+          ccmslib,
+          charge
+        ) |>
+          tidyft::mutate_vars(
+            is.character,
+            .func = function(x) {
+              tidytable::na_if(x, "")
+            }
+          )
+
+        df_clean <- df_meta |>
+          dplyr::filter(!is.na(inchikey)) |>
+          dplyr::filter(fragments > 5) |>
+          dplyr::filter(fragments <= 1000) |>
+          dplyr::filter(!grepl(
+            pattern = "QQQ",
+            x = instrument,
+            fixed = TRUE
+          )) |>
+          dplyr::mutate(mass = pepmass) |>
+          tidyr::separate(
+            col = mass,
+            sep = "\\.",
+            into = c("a", "b")
+          ) |>
+          dplyr::filter(!is.na(b)) |>
+          dplyr::filter(stringr::str_length(b) > 1) |>
+          dplyr::select(-a, -b) |>
+          dplyr::mutate(inchikey_2D = gsub(
+            pattern = "-.*",
+            replacement = "",
+            x = inchikey
+          )) |>
+          dplyr::distinct(inchikey_2D, adduct, .keep_all = TRUE) |>
+          dplyr::mutate(mz = pepmass) |>
+          dplyr::group_by(inchikey_2D) |>
+          ## Weird way to have some kind of retention time
+          dplyr::mutate(rt = dplyr::cur_group_id()) |>
+          dplyr::ungroup()
+
+        df_clean_neg <- df_clean |>
+          dplyr::filter(grepl(
+            pattern = "-",
+            x = charge,
+            fixed = TRUE
+          )) |>
+          dplyr::mutate(feature_id = dplyr::row_number())
+
+        df_clean_pos <- df_clean |>
+          dplyr::anti_join(df_clean_neg) |>
+          dplyr::mutate(feature_id = dplyr::row_number())
+
+        sp_pos <- sp_clean[sp_clean$SPECTRUMID %in% df_clean_pos$ccmslib]
+        sp_neg <- sp_clean[sp_clean$SPECTRUMID %in% df_clean_neg$ccmslib]
+        sp_pos$feature_id <- df_clean_pos$feature_id
+        sp_neg$feature_id <- df_clean_neg$feature_id
+        sp_pos$spectrum_id <- df_clean_pos$feature_id
+        sp_neg$spectrum_id <- df_clean_neg$feature_id
+
+        spectra_harmonized_pos <- sp_pos |>
+          extract_spectra() |>
+          dplyr::mutate(polarity = "pos") |>
+          harmonize_spectra(
+            col_ce = NA,
+            col_ci = NA,
+            col_em = "PARENT_MASS",
+            col_in = "inchi",
+            col_io = NA,
+            col_ik = "inchikey",
+            col_il = NA,
+            # col_mf = "formula",
+            col_mf = NA,
+            col_na = "name",
+            col_po = "polarity",
+            col_sm = "smiles",
+            col_sn = NA,
+            col_si = "spectrum_id",
+            col_sp = NA,
+            col_sy = NA,
+            col_xl = NA,
+            mode = "pos"
+          )
+
+        spectra_harmonized_neg <- sp_neg |>
+          extract_spectra() |>
+          dplyr::mutate(polarity = "neg") |>
+          harmonize_spectra(
+            col_ce = NA,
+            col_ci = NA,
+            col_em = "PARENT_MASS",
+            col_in = "inchi",
+            col_io = NA,
+            col_ik = "inchikey",
+            col_il = NA,
+            # col_mf = "formula",
+            col_mf = NA,
+            col_na = "name",
+            col_po = "polarity",
+            col_sm = "smiles",
+            col_sn = NA,
+            col_si = "spectrum_id",
+            col_sp = NA,
+            col_sy = NA,
+            col_xl = NA,
+            mode = "neg"
+          )
+
+        spectra_harmonized_pos$acquisitionNum <-
+          spectra_harmonized_pos$spectrum_id |>
+          as.integer()
+        spectra_harmonized_neg$acquisitionNum <-
+          spectra_harmonized_neg$spectrum_id |>
+          as.integer()
+
+        log_debug("Exporting")
+        spectra_harmonized_pos |>
+          Spectra::Spectra() |>
+          Spectra::export(
+            backend = MsBackendMgf::MsBackendMgf(),
+            file = mgf_pos_path
+          )
+        spectra_harmonized_neg |>
+          Spectra::Spectra() |>
+          Spectra::export(
+            backend = MsBackendMgf::MsBackendMgf(),
+            file = mgf_neg_path
+          )
+        df_clean_pos |>
+          export_output(meta_pos_path)
+        df_clean_neg |>
+          export_output(meta_neg_path)
+
+        return(
+          c(
+            "spectra_pos" = benchmark_path_mgf_pos,
+            "spectra_neg" = benchmark_path_mgf_neg,
+            "meta_pos" = "data/interim/benchmark/benchmark_meta_pos.tsv",
+            "meta_neg" = "data/interim/benchmark/benchmark_meta_neg.tsv"
+          )
         )
       }
     ),