taxonomicallyinformedannotation · Adafede · Jul 3, 2024 · Jul 3, 2024 · Jul 3, 2024
diff --git a/R/annotate_masses.R b/R/annotate_masses.R
@@ -35,18 +35,18 @@
 #'
 #' @examples NULL
 annotate_masses <-
 function(features = get_params(step = "annotate_masses")$files$features$prepared,
 filter_nitro = get_params(step = "annotate_masses")$options$nitrogen_rule,
 output_annotations = get_params(step = "annotate_masses")$files$annotations$prepared$structural$ms1,
 output_edges = get_params(step = "annotate_masses")$files$networks$spectral$edges$raw,
 name_source = get_params(step = "annotate_masses")$names$source,
 name_target = get_params(step = "annotate_masses")$names$target,
 library = get_params(step = "annotate_masses")$files$libraries$sop$merged$keys,
 str_stereo = get_params(step = "annotate_masses")$files$libraries$sop$merged$structures$stereo,
 str_met = get_params(step = "annotate_masses")$files$libraries$sop$merged$structures$metadata,
 str_nam = get_params(step = "annotate_masses")$files$libraries$sop$merged$structures$names,
 str_tax_cla = get_params(step = "annotate_masses")$files$libraries$sop$merged$structures$taxonomies$cla,
 str_tax_npc = get_params(step = "annotate_masses")$files$libraries$sop$merged$structures$taxonomies$npc,
 adducts_list = get_params(step = "annotate_masses")$ms$adducts,
 adducts_masses_list = system.file("extdata",
 "adducts.tsv",
@@ -437,7 +437,7 @@
  )
  rm(df_adducted, df_nl_min)
 
- # TODO dictionary of adducts (example 2H2O in mzmine)
+ # ISSUE see #141 dictionary of adducts (example 2H2O in mzmine)
 
  df_addlossed_min <- df_addlossed |>
  tidytable::rowwise() |>
@@ -466,8 +466,6 @@
  df_addlossed_rdy <- df_addlossed_min_1 |>
  tidytable::bind_rows(df_addlossed_min_2)
 
- # TODO if same, say unrecognized and switch to M+H or M-H by default
-
  log_debug("joining within given mz tol to exact mass library \n")
  df_addlossed_em <- df_addlossed_rdy |>
  dplyr::inner_join(df_add_em,
@@ -520,7 +518,7 @@
  )
  )
 
- ## TODO This will then be externalized somehow
+ ## TODO This should be externalized somehow
  forbidden_adducts <- c(
  "[M-H2O (water)+H2O-H]-",
  "[M-H3O4P (phosphoric)+H3O4P-H]-",

diff --git a/R/annotate_spectra.R b/R/annotate_spectra.R
@@ -97,7 +97,7 @@ annotate_spectra <- function(input = get_params(step = "annotate_spectra")$files
 
  query_precursors <- spectra@backend@spectraData$precursorMz
  query_spectra <- spectra@backend@peaksData
- ## TODO find a way to have consistency in spectrum IDs
+ ## ISSUE see #148 find a way to have consistency in spectrum IDs
  query_ids <- spectra@backend@spectraData$acquisitionNum
  if (is.null(query_ids)) {
  query_ids <- spectra@backend@spectraData$spectrum_id

diff --git a/R/complement_metadata_structures.R b/R/complement_metadata_structures.R
@@ -303,7 +303,8 @@ complement_metadata_structures <- function(
  )
  rm(met_i, met_s, nam_i, nam_s, stereo_i, stereo_s, tax_cla, tax_npc)
 
- ## TODO if (quickmode == FALSE){...}
+ ## ISSUE see #19
+ # if (quickmode == FALSE){...}
 
  return(table_final)
 }
diff --git a/R/create_edges_spectra.R b/R/create_edges_spectra.R
@@ -87,7 +87,7 @@ create_edges_spectra <- function(
  tidytable::everything()
  )
 
- ## TODO find a way to have consistency in spectrum IDs
+ ## ISSUE see #148 find a way to have consistency in spectrum IDs
  idz <- spectra@backend@spectraData$acquisitionNum
  rm(spectra)
  edges <- edges |>

diff --git a/R/filter_annotations.R b/R/filter_annotations.R
@@ -80,7 +80,7 @@ filter_annotations <-
  tidytable::distinct(-candidate_structure_error_rt, -rt_target,
  .keep_all = TRUE
  ) |>
- ## TODO adapt for types and improve the * 3
+ ## ISSUE see #149 adapt for types and improve the * 3
  tidytable::filter(abs(candidate_structure_error_rt) <= abs(tolerance_rt * 3) | is.na(candidate_structure_error_rt)) |>
  tidytable::select(-rt_target, -type)
  } else {

diff --git a/R/install_latest_version.R b/R/install_latest_version.R
@@ -51,7 +51,6 @@ install_latest_version <- function() {
  } else {
  local_version <- pak::pkg_status("timaR")$version[1]
  }
- # TODO not ideal
  remote_version <- readLines(
  paste0(
  "https://raw.githubusercontent.com/taxonomicallyinformedannotation/tima-r/",

diff --git a/R/prepare_annotations_sirius.R b/R/prepare_annotations_sirius.R
@@ -171,7 +171,7 @@ prepare_annotations_sirius <-
  tidytable::left_join(formulas_prepared) |>
  tidytable::left_join(canopus_prepared) |>
  tidytable::left_join(denovo_prepared) |>
- # TODO add de novo and spectral
+ # TODO add spectral
  tidytable::distinct() |>
  tidytable::mutate(
  candidate_structure_tax_cla_chemontid = NA,

diff --git a/R/prepare_libraries_rt.R b/R/prepare_libraries_rt.R
@@ -153,7 +153,7 @@ prepare_libraries_rt <-
  "We would recommend you adding them but will try completing.",
  "We will query them on the fly, this might take some time."
  )
- ## TODO change with a small dependency
+ ## ISSUE see #19
  smiles <- unique(df_missing$smiles)
 
  get_inchikey <- function(smiles, toolkit = "rdkit") {

diff --git a/R/prepare_libraries_sop_ecmdb.R b/R/prepare_libraries_sop_ecmdb.R
@@ -46,7 +46,7 @@ prepare_libraries_sop_ecmdb <-
  from = 1,
  to = 14
  ),
- ## TODO compute it
+ ## ISSUE see #19
  structure_smiles_2D = NA_character_
  ) |>
  tidytable::rename(

diff --git a/R/prepare_libraries_sop_hmdb.R b/R/prepare_libraries_sop_hmdb.R
@@ -72,7 +72,7 @@ prepare_libraries_sop_hmdb <-
  from = 1,
  to = 14
  ),
- ## TODO compute it
+ ## ISSUE see #19
  structure_smiles_2D = NA_character_,
  structure_exact_mass = NA_real_
  ) |>

diff --git a/R/prepare_libraries_sop_merged.R b/R/prepare_libraries_sop_merged.R
@@ -138,17 +138,11 @@ prepare_libraries_sop_merged <-
  table_structures_taxonomy_cla <- tables$str_tax_cla
  table_structures_taxonomy_npc <- tables$str_tax_npc
 
- log_debug(x = "Completing structures metadata")
- log_debug(x = "TODO")
-
- log_debug(x = "Completing structures names")
- log_debug(x = "TODO")
-
- log_debug(x = "Completing structures taxonomy (classyfire)")
- log_debug(x = "TODO")
-
- log_debug(x = "Completing structures taxonomy (NPC)")
- log_debug(x = "TODO")
+ ## ISSUE see #19
+ # log_debug(x = "Completing structures metadata")
+ # log_debug(x = "Completing structures names")
+ # log_debug(x = "Completing structures taxonomy (classyfire)")
+ # log_debug(x = "Completing structures taxonomy (NPC)")
 
  ## If filter is TRUE,
  ## filter the library based on the specified level and value

diff --git a/R/prepare_params.R b/R/prepare_params.R
@@ -57,7 +57,6 @@ prepare_params <- function(params_small = get_params(step = "prepare_params"),
  fil_lib_sop_pre_hmd <- params_advanced$files$libraries$sop$prepared$hmdb
  fil_lib_sop_pre_lot <- params_advanced$files$libraries$sop$prepared$lotus
  fil_lib_sop_pre_rt <- params_advanced$files$libraries$sop$prepared$rt
- # TODO Docopt
  fil_lib_sop_mer_key <- params_advanced$files$libraries$sop$merged$keys
  fil_lib_sop_mer_org_nam <- params_advanced$files$libraries$sop$merged$organisms$names
  fil_lib_sop_mer_org_tax_ott <- params_advanced$files$libraries$sop$merged$organisms$taxonomies$ott
@@ -66,7 +65,6 @@ prepare_params <- function(params_small = get_params(step = "prepare_params"),
  fil_lib_sop_mer_str_nam <- params_advanced$files$libraries$sop$merged$structures$names
  fil_lib_sop_mer_str_tax_cla <- params_advanced$files$libraries$sop$merged$structures$taxonomies$cla
  fil_lib_sop_mer_str_tax_npc <- params_advanced$files$libraries$sop$merged$structures$taxonomies$npc
- # TODO Docopt
  fil_lib_spe_exp_neg <- params_advanced$files$libraries$spectral$exp$neg
  fil_lib_spe_exp_pos <- params_advanced$files$libraries$spectral$exp$pos
  fil_lib_spe_exp_raw <- params_advanced$files$libraries$spectral$exp$raw
@@ -472,7 +470,6 @@ prepare_params <- function(params_small = get_params(step = "prepare_params"),
  org_fil_val
  },
  prepare_libraries_spectra = {
- # TODO see layers
  yamls_params$prepare_libraries_spectra$files$libraries$spectral$exp$neg <-
  fil_lib_spe_exp_neg
  yamls_params$prepare_libraries_spectra$files$libraries$spectral$exp$pos <-

diff --git a/R/select_sirius_columns.R b/R/select_sirius_columns.R
@@ -110,7 +110,7 @@ select_sirius_columns_structures <- function(df, sirius_version) {
  "candidate_structure_inchikey_no_stereo" = "InChIkey2D",
  "candidate_structure_molecular_formula" = "molecularFormula",
  "candidate_structure_xlogp" = "xlogp",
- # TODO DOC
+ # ISSUE see #147
  "candidate_score_sirius_confidence" = switch(sirius_version,
  "5" = "ConfidenceScore",
  "6" = "ConfidenceScoreApproximate"

diff --git a/R/weight_bio.R b/R/weight_bio.R
@@ -433,7 +433,7 @@ weight_bio <-
  ) |>
  tidytable::left_join(df0) |>
  log_pipe("... calculating weighted biological score \n") |>
- ## TODO suboptimal
+ ## ISSUE see #146
  tidytable::mutate(interim = -10 / as.numeric(candidate_score_sirius_csi)) |>
  tidytable::mutate(interim_2 = ifelse(test = interim > 1,
  yes = 1,

diff --git a/codemeta.json b/codemeta.json
@@ -591,7 +591,7 @@
  "SystemRequirements": null
  },
  "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
- "fileSize": "4379.259KB",
+ "fileSize": "4379.057KB",
  "citation": [
  {
  "@type": "ScholarlyArticle",

diff --git a/inst/pipelines/_targets.R b/inst/pipelines/_targets.R
@@ -1351,7 +1351,7 @@ list(
  )
  }
  ),
- ## TODO ADD  GET HMDB
+ ## TODO ADD GET HMDB
  tar_target(
  name = lib_sop_lot,
  format = "file",

diff --git a/tests/testthat/test-functions.R b/tests/testthat/test-functions.R
@@ -383,7 +383,7 @@ test_that(desc = "Test functions", code = {
  prepare_features_tables()
 
  ## Performing MS1 annotation
- ## TODO improve this
+ ## TODO check values later on
  calculate_mass_from_adduct(adduct_string = "[2M1-2H2O+NaCl+H]2+", mass = 123.456)
  calculate_mass_from_adduct(adduct_string = "[M+Na]+", mass = 123.456)
  calculate_mass_from_adduct(adduct_string = "[M+H]+", mass = 123.456)