Replace internal functions by Spectra equivalents

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tima
 Title: Taxonomically Informed Metabolite Annotation
-Version: 2.10.0
+Version: 2.10.1
 Authors@R: c(
     person("Adriano", "Rutz", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0443-9902")),
@@ -93,11 +93,7 @@ Collate:
     'parse_adduct.R'
     'calculate_mass_of_m.R'
     'annotate_masses.R'
-    'keep_peaks.R'
     'sanitize_spectra.R'
-    'remove_above_precursor.R'
-    'normalize_peaks.R'
-    'cleanup_spectra.R'
     'import_spectra.R'
     'annotate_spectra.R'
     'benchmark_taxize_spectra.R'

NAMESPACE

@@ -8,7 +8,6 @@ export(calculate_mass_of_m)
 export(clean_bio)
 export(clean_chemo)
 export(clean_collapse)
-export(cleanup_spectra)
 export(columns_model)
 export(complement_metadata_structures)
 export(create_components)
@@ -46,11 +45,9 @@ export(harmonize_names_sirius)
 export(harmonize_spectra)
 export(import_spectra)
 export(install)
-export(keep_peaks)
 export(load_yaml_files)
 export(log_debug)
 export(log_pipe)
-export(normalize_peaks)
 export(parse_adduct)
 export(parse_cli_params)
 export(parse_yaml_params)
@@ -72,7 +69,6 @@ export(prepare_libraries_spectra)
 export(prepare_params)
 export(prepare_taxa)
 export(read_from_sirius_zip)
-export(remove_above_precursor)
 export(replace_id)
 export(round_reals)
 export(run_app)
@@ -101,8 +97,11 @@ importFrom(Spectra,dropNaSpectraVariables)
 importFrom(Spectra,filterEmptySpectra)
 importFrom(Spectra,filterFourierTransformArtefacts)
 importFrom(Spectra,filterIntensity)
+importFrom(Spectra,filterMsLevel)
 importFrom(Spectra,filterPrecursorCharge)
+importFrom(Spectra,filterPrecursorPeaks)
 importFrom(Spectra,reduceSpectra)
+importFrom(Spectra,scalePeaks)
 importFrom(crayon,blue)
 importFrom(crayon,cyan)
 importFrom(crayon,green)

NEWS.md

@@ -1,5 +1,9 @@
 # tima
 
+# tima 2.10.1
+
+* Replaced internal functions by `Spectra` equivalents (#166)
+
 # tima 2.10.0
 
 * Added alt text to vignettes

R/annotate_spectra.R

@@ -2,11 +2,8 @@ import::from(dplyr, join_by, .into = environment())
 import::from(msentropy, calculate_entropy_similarity, .into = environment())
 import::from(msentropy, calculate_spectral_entropy, .into = environment())
 import::from(pbapply, pblapply, .into = environment())
-import::from(Spectra, addProcessing, .into = environment())
 import::from(Spectra, applyProcessing, .into = environment())
 import::from(Spectra, concatenateSpectra, .into = environment())
-import::from(Spectra, filterIntensity, .into = environment())
-import::from(Spectra, filterPrecursorCharge, .into = environment())
 import::from(tidytable, any_of, .into = environment())
 import::from(tidytable, arrange, .into = environment())
 import::from(tidytable, as_tidytable, .into = environment())
@@ -31,11 +28,8 @@ import::from(tidytable, tidytable, .into = environment())
 #' @importFrom msentropy calculate_entropy_similarity
 #' @importFrom msentropy calculate_spectral_entropy
 #' @importFrom pbapply pblapply
-#' @importFrom Spectra addProcessing
 #' @importFrom Spectra applyProcessing
 #' @importFrom Spectra concatenateSpectra
-#' @importFrom Spectra filterIntensity
-#' @importFrom Spectra filterPrecursorCharge
 #' @importFrom tidytable any_of
 #' @importFrom tidytable arrange
 #' @importFrom tidytable as_tidytable
@@ -52,9 +46,6 @@ import::from(tidytable, tidytable, .into = environment())
 #' @include get_params.R
 #' @include harmonize_adducts.R
 #' @include import_spectra.R
-#' @include normalize_peaks.R
-#' @include remove_above_precursor.R
-#' @include sanitize_spectra.R
 #'
 #' @param input Query file containing spectra. Currently an '.mgf' file
 #' @param library Library containing spectra to match against.
@@ -94,12 +85,12 @@ annotate_spectra <- function(input = get_params(step = "annotate_spectra")$files
 
   log_debug("Loading spectra...")
   spectra <- input |>
-    import_spectra() |>
-    filterPrecursorCharge(z = if (polarity == "pos") {
-      c(1, 2, 3)
-    } else {
-      c(-1, -2, -3)
-    })
+    import_spectra(
+      cutoff = qutoff,
+      dalton = dalton,
+      polarity = polarity,
+      ppm = ppm
+    )
 
   df_empty <- data.frame(
     feature_id = NA,
@@ -120,24 +111,16 @@ annotate_spectra <- function(input = get_params(step = "annotate_spectra")$files
   if (length(spectra) > 0) {
     log_debug("Loading spectral library")
     spectral_library <- unlist(library) |>
-      lapply(FUN = import_spectra) |>
-      concatenateSpectra() |>
-      sanitize_spectra() |>
-      addProcessing(remove_above_precursor(),
-        spectraVariables = c("precursorMz")
-      ) |>
-      addProcessing(normalize_peaks()) |>
-      applyProcessing()
-
-    log_debug("Applying initial intensity filter to query spectra")
-    spectra <- spectra |>
-      sanitize_spectra() |>
-      filterIntensity(intensity = c(qutoff, Inf)) |>
-      addProcessing(remove_above_precursor(),
-        spectraVariables = c("precursorMz")
+      lapply(
+        FUN = import_spectra,
+        cutoff = qutoff,
+        dalton = dalton,
+        polarity = polarity,
+        ppm = ppm,
+        sanitize = FALSE
       ) |>
-      addProcessing(normalize_peaks()) |>
-      applyProcessing()
+      lapply(FUN = applyProcessing) |>
+      concatenateSpectra()
 
     query_precursors <- spectra@backend@spectraData$precursorMz
     query_spectra <- spectra@backend@peaksData

R/create_edges_spectra.R

@@ -1,7 +1,5 @@
 import::from(msentropy, calculate_spectral_entropy, .into = environment())
 import::from(pbapply, pblapply, .into = environment())
-import::from(Spectra, addProcessing, .into = environment())
-import::from(Spectra, applyProcessing, .into = environment())
 import::from(tidyfst, rn_col, .into = environment())
 import::from(tidytable, any_of, .into = environment())
 import::from(tidytable, bind_rows, .into = environment())
@@ -21,8 +19,6 @@ import::from(tidytable, tidytable, .into = environment())
 #'
 #' @importFrom msentropy calculate_spectral_entropy
 #' @importFrom pbapply pblapply
-#' @importFrom Spectra addProcessing
-#' @importFrom Spectra applyProcessing
 #' @importFrom tidyfst rn_col
 #' @importFrom tidytable any_of
 #' @importFrom tidytable bind_rows
@@ -38,9 +34,6 @@ import::from(tidytable, tidytable, .into = environment())
 #' @include create_edges.R
 #' @include get_params.R
 #' @include import_spectra.R
-#' @include normalize_peaks.R
-#' @include remove_above_precursor.R
-#' @include sanitize_spectra.R
 #'
 #' @param input Query file containing spectra. Currently an '.mgf' file
 #' @param output Output file.
@@ -69,16 +62,12 @@ create_edges_spectra <- function(input = get_params(step = "create_edges_spectra
 
   log_debug("Loading spectra...")
   spectra <- input |>
-    import_spectra()
+    import_spectra(
+      cutoff = qutoff,
+      dalton = dalton,
+      ppm = ppm
+    )
   if (length(spectra) > 1) {
-    spectra <- spectra |>
-      sanitize_spectra(cutoff = qutoff) |>
-      # addProcessing(remove_above_precursor(),
-      #   spectraVariables = c("precursorMz")
-      # ) |>
-      addProcessing(normalize_peaks()) |>
-      applyProcessing()
-
     log_debug("Performing spectral comparison")
     log_debug("As we do not limit the precursors delta,
       expect a (relatively) long processing time.")

R/get_example_files.R

@@ -7,28 +7,42 @@
 #' @include go_to_cache.R
 #' @include parse_yaml_paths.R
 #'
+#' @param example The example(s) you want to download
+#'
 #' @return Example files.
 #'
 #' @export
 #'
 #' @examples NULL
-get_example_files <- function() {
-  go_to_cache()
-  message("Features")
-  get_file(
-    url = tima::parse_yaml_paths()$urls$examples$features,
-    export = tima::parse_yaml_paths()$data$source$features
-  )
-  message("Metadata")
-  get_file(
-    url = tima::parse_yaml_paths()$urls$examples$metadata,
-    export = tima::parse_yaml_paths()$data$source$metadata
-  )
-  message("Sirius")
-  get_example_sirius()
-  message("Spectra")
-  get_file(
-    url = tima::parse_yaml_paths()$urls$examples$spectra,
-    export = tima::parse_yaml_paths()$data$source$spectra
+get_example_files <- function(example = c("features", "metadata", "sirius", "spectra")) {
+  stopifnot(
+    "Example files available are `features`, `metadata`, `sirius` and `spectra`." =
+      example %in% c("features", "metadata", "sirius", "spectra")
   )
+  go_to_cache()
+  if ("features" %in% example) {
+    message("Features")
+    get_file(
+      url = tima::parse_yaml_paths()$urls$examples$features,
+      export = tima::parse_yaml_paths()$data$source$features
+    )
+  }
+  if ("metadata" %in% example) {
+    message("Metadata")
+    get_file(
+      url = tima::parse_yaml_paths()$urls$examples$metadata,
+      export = tima::parse_yaml_paths()$data$source$metadata
+    )
+  }
+  if ("sirius" %in% example) {
+    message("Sirius")
+    get_example_sirius()
+  }
+  if ("spectra" %in% example) {
+    message("Spectra")
+    get_file(
+      url = tima::parse_yaml_paths()$urls$examples$spectra,
+      export = tima::parse_yaml_paths()$data$source$spectra
+    )
+  }
 }

R/import_spectra.R

@@ -14,16 +14,26 @@ import::from(stringi, stri_replace_all_regex, .into = environment())
 #' @importFrom Spectra Spectra
 #' @importFrom stringi stri_replace_all_regex
 #'
-#' @include cleanup_spectra.R
+#' @include sanitize_spectra.R
 #'
 #' @param file File path of the spectrum file to be imported
+#' @param cutoff Absolute minimal intensity
+#' @param dalton Dalton tolerance
+#' @param polarity Polarity
+#' @param ppm PPM tolerance
+#' @param sanitize Flag indicating whether to sanitize. Default TRUE
 #'
 #' @return Spectra object containing the imported spectra
 #'
 #' @export
 #'
 #' @examples NULL
-import_spectra <- function(file) {
+import_spectra <- function(file,
+                           cutoff = 0,
+                           dalton = 0.01,
+                           polarity = NA,
+                           ppm = 10,
+                           sanitize = TRUE) {
   file_ext <-
     stri_replace_all_regex(
       str = file,
@@ -32,19 +42,17 @@ import_spectra <- function(file) {
       vectorize_all = FALSE
     )
 
-  switch(
+  spectra <- switch(
     EXPR = file_ext,
     "mgf" = {
       readMgf(f = file) |>
         # TODO Change as soon as R 4.4.0 becomes oldrel
         # readMgfSplit(f = file) |>
-        Spectra() |>
-        cleanup_spectra()
+        Spectra()
     },
     "msp" = {
       readMsp(f = file) |>
-        Spectra() |>
-        cleanup_spectra()
+        Spectra()
     },
     # "sqlite" = {
     #   CompDb(x = file) |>
@@ -54,8 +62,17 @@ import_spectra <- function(file) {
     "rds" = {
       readRDS(file = file) |>
         data.frame() |>
-        Spectra() |>
-        cleanup_spectra()
+        Spectra()
     }
   )
+  if (sanitize) {
+    spectra <- spectra |>
+      sanitize_spectra(
+        cutoff = cutoff,
+        dalton = dalton,
+        polarity = polarity,
+        ppm = ppm
+      )
+  }
+  return(spectra)
 }