fix spectral libraries names (#82)

taxonomicallyinformedannotation · Sep 6, 2023 · 2c71f31 · 2c71f31
1 parent 254cc41
commit 2c71f31
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Showing 4 changed files with 34 additions and 13 deletions.
diff --git a/R/annotate_spectra.R b/R/annotate_spectra.R
@@ -271,9 +271,9 @@ annotate_spectra <- function(input = params$files$spectral$raw,
     if (is.null(lib_smiles2D)) {
       lib_smiles2D <- rep(NA_character_, length(spectral_library))
     }
-    lib_name <- spectral_library@backend@spectraData$name
-    if (is.null(lib_name)) {
-      lib_name <- rep(NA_character_, length(spectral_library))
+    lib_library <- spectral_library@backend@spectraData$library
+    if (is.null(lib_library)) {
+      lib_library <- rep(NA_character_, length(spectral_library))
     }
     lib_mf <- spectral_library@backend@spectraData$formula
     if (is.null(lib_mf)) {
@@ -283,6 +283,10 @@ annotate_spectra <- function(input = params$files$spectral$raw,
     if (is.null(lib_mass)) {
       lib_mass <- rep(NA_real_, length(spectral_library))
     }
+    lib_name <- spectral_library@backend@spectraData$name
+    if (is.null(lib_name)) {
+      lib_name <- rep(NA_character_, length(spectral_library))
+    }
     lib_xlogp <- spectral_library@backend@spectraData$xlogp
     if (is.null(lib_xlogp)) {
       lib_xlogp <- rep(NA_real_, length(spectral_library))
@@ -294,9 +298,10 @@ annotate_spectra <- function(input = params$files$spectral$raw,
       "target_inchikey_no_stereo" = lib_inchikey2D,
       "target_smiles" = lib_smiles,
       "target_smiles_no_stereo" = lib_smiles2D,
-      "target_name" = lib_name,
+      "target_library" = lib_library,
       "target_formula" = lib_mf,
       "target_exactmass" = lib_mass,
+      "target_name" = lib_name,
       "target_xlogp" = lib_xlogp,
       "target_precursorMz" = lib_precursors
     )
@@ -325,6 +330,7 @@ annotate_spectra <- function(input = params$files$spectral$raw,
       tidytable::select(tidytable::any_of(
         c(
           "feature_id",
+          "candidate_library" = "target_library",
           "candidate_structure_error_mz",
           "candidate_structure_name" = "target_name",
           "candidate_structure_inchikey_no_stereo",

diff --git a/R/harmonize_spectra.R b/R/harmonize_spectra.R
@@ -3,6 +3,7 @@
 #' @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_ce Name of the collision energy in mgf
 #' @param col_ci Name of the compound id in mgf
@@ -27,6 +28,10 @@
 #'
 #' @examples NULL
 harmonize_spectra <- function(spectra,
+                              metad = get(
+                                "metad",
+                                envir = parent.frame()
+                              ),
                               mode,
                               col_ce = get(
                                 "col_ce",
@@ -142,11 +147,21 @@ harmonize_spectra <- function(spectra,
   spectra_filtered <- spectra |>
     data.frame() |>
     tidytable::as_tidytable() |>
-    tidytable::filter(grepl(
-      pattern = mode,
-      x = !!as.name(col_po),
-      ignore.case = TRUE
-    )) |>
+    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(
       tidytable::any_of(c(columns_full)),
       precursorCharge,
@@ -182,6 +197,7 @@ harmonize_spectra <- function(spectra,
       intensity
     ) |>
     tidytable::mutate(
+      library = metad,
       exactmass = as.numeric(exactmass),
       spectrum_id = ifelse(
         test = is.na(spectrum_id),

diff --git a/R/prepare_annotations_spectra.R b/R/prepare_annotations_spectra.R
@@ -50,6 +50,7 @@ prepare_annotations_spectra <-
       tidytable::filter(!is.na(feature_id)) |>
       tidytable::distinct(
         feature_id,
+        candidate_library,
         candidate_spectrum_entropy,
         candidate_structure_error_mz,
         candidate_structure_name,
@@ -63,8 +64,6 @@ prepare_annotations_spectra <-
       ) |>
       ## Add new columns
       tidytable::mutate(
-        candidate_library = "ISDB",
-        ## TODO candidate_library_type = "TODO",
         candidate_structure_exact_mass =
           as.numeric(candidate_structure_exact_mass),
         candidate_structure_tax_npc_01pat = NA_character_,

diff --git a/R/prepare_libraries_spectra.R b/R/prepare_libraries_spectra.R
@@ -12,7 +12,7 @@
 #' @param input File containing spectra
 #' @param output Output file
 #' @param polarity MS polarity
-#' @param metad Optional. Metadata as in 'CompoundDb' package
+#' @param metad Metadata to identify the library
 #' @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
@@ -40,7 +40,7 @@ prepare_libraries_spectra <-
   function(input = params$files$libraries$spectral$exp$raw,
            output = params$files$libraries$spectral$exp,
            polarity = params$ms$polarity,
-           metad = NULL,
+           metad = "myLib",
            col_ce = params$names$mgf$collision_energy,
            col_ci = params$names$mgf$compound_id,
            col_em = params$names$mgf$exact_mass,