Fix #166

DESCRIPTION

@@ -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 +111,15 @@ 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
  ) |>
- 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/import_spectra.R

@@ -14,16 +14,24 @@ 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
 #'
 #' @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) {
  file_ext <-
  stri_replace_all_regex(
  str = file,
@@ -39,12 +47,22 @@ import_spectra <- function(file) {
  # TODO Change as soon as R 4.4.0 becomes oldrel
  # readMgfSplit(f = file) |>
  Spectra() |>
- cleanup_spectra()
+ sanitize_spectra(
+ cutoff = cutoff,
+ dalton = dalton,
+ polarity = polarity,
+ ppm = ppm
+ )
  },
  "msp" = {
  readMsp(f = file) |>
  Spectra() |>
- cleanup_spectra()
+ sanitize_spectra(
+ cutoff = cutoff,
+ dalton = dalton,
+ polarity = polarity,
+ ppm = ppm
+ )
  },
  # "sqlite" = {
  # CompDb(x = file) |>
@@ -55,7 +73,12 @@ import_spectra <- function(file) {
  readRDS(file = file) |>
  data.frame() |>
  Spectra() |>
- cleanup_spectra()
+ sanitize_spectra(
+ cutoff = cutoff,
+ dalton = dalton,
+ polarity = polarity,
+ ppm = ppm
+ )
  }
  )
 }