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taxonomicallyinformedannotation · Feb 7, 2023 · 54b3efe · 54b3efe
1 parent fafb575
commit 54b3efe
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Showing 3 changed files with 80 additions and 143 deletions.
diff --git a/R/clean_chemo.R b/R/clean_chemo.R
@@ -189,6 +189,7 @@ clean_chemo <-
  c(
  -reference_doi,
  -structure_name,
+ -structure_xlogp,
  -structure_01pathway,
  -structure_02superclass,
  -structure_03class
@@ -198,14 +199,15 @@ clean_chemo <-
  c(
  reference_doi,
  structure_name,
+ structure_xlogp,
  structure_01pathway,
  structure_02superclass,
  structure_03class
  ),
  ~ gsub(
  pattern = "\\bNA\\b",
  replacement = "",
- x = paste(.x, collapse = "$")
+ x = paste(unique(.x), collapse = "$")
  )
  )) |>
  dplyr::group_by(feature_id) |>
@@ -218,143 +220,80 @@ clean_chemo <-
  x = paste(.x, collapse = "|")
  )
  )) |>
- dplyr::select(
- -rt,
- -mz
- )
+ dplyr::select(-rt, -mz)
 
  df5b <- dplyr::left_join(df5a, df4b) |>
  dplyr::distinct()
 
- if (!any(names(metadata_table_spectral_annotation) == "rt")) {
- df6 <- metadata_table_spectral_annotation |>
- dplyr::distinct(
- feature_id,
- component_id,
- mz
- )
- } else {
- df6 <- metadata_table_spectral_annotation |>
- dplyr::distinct(
- feature_id,
- component_id,
- mz,
- rt
- )
- }
+ df6 <- metadata_table_spectral_annotation |>
+ dplyr::select(dplyr::any_of(c(
+ "feature_id",
+ "component_id",
+ "mz",
+ "rt"
+ ))) |>
+ dplyr::distinct()
 
- if (!any(names(metadata_table_spectral_annotation) == "rt")) {
- df7 <- dplyr::left_join(df6, df5b) |>
- dplyr::arrange(feature_id) |>
- dplyr::mutate_all(as.character) |>
- dplyr::mutate_all(dplyr::na_if, "") |>
- dplyr::select(
- feature_id,
- component_id,
- mz,
- molecular_formula,
- mz_error,
- library,
- smiles_2D,
- inchikey_2D,
- score_initialNormalized,
- score_biological,
- score_chemical,
- score_final,
- rank_initial,
- rank_final,
- best_candidate_organism,
- best_candidate_structure,
- consensus_structure_pat,
- consistency_structure_pat,
- consensus_structure_sup,
- consistency_structure_sup,
- consensus_structure_cla,
- consistency_structure_cla,
- reference_doi
+ df7 <- dplyr::left_join(df6, df5b) |>
+ dplyr::arrange(feature_id) |>
+ dplyr::mutate_all(as.character) |>
+ dplyr::mutate_all(dplyr::na_if, "") |>
+ dplyr::select(dplyr::any_of(
+ c(
+ "feature_id",
+ "component_id",
+ "mz",
+ "rt",
+ "molecular_formula",
+ "mz_error",
+ "library",
+ "smiles_2D",
+ "inchikey_2D",
+ "score_initialNormalized",
+ "score_biological",
+ "score_chemical",
+ "score_final",
+ "rank_initial",
+ "rank_final",
+ "best_candidate_organism",
+ "best_candidate_structure",
+ "consensus_structure_pat",
+ "consistency_structure_pat",
+ "consensus_structure_sup",
+ "consistency_structure_sup",
+ "consensus_structure_cla",
+ "consistency_structure_cla",
+ "reference_doi"
  )
+ ))
 
-  log_debug("adding consensus again to droped candidates \n")
-  df8 <- df7 |>
-  dplyr::filter(!is.na(inchikey_2D))
+ log_debug("adding consensus again to droped candidates \n")
+ df8 <- df7 |>
+ dplyr::filter(!is.na(inchikey_2D))
 
-  df9 <- df7 |>
-  dplyr::filter(is.na(inchikey_2D))
+ df9 <- df7 |>
+ dplyr::filter(is.na(inchikey_2D))
 
- df10 <- dplyr::left_join(
- df9,
- annotationTableWeightedChemo |>
- dplyr::mutate_all(as.character)
- ) |>
- dplyr::select(
- feature_id,
- component_id,
- mz,
- consensus_structure_pat,
- consistency_structure_pat,
- consensus_structure_sup,
- consistency_structure_sup,
- consensus_structure_cla,
- consistency_structure_cla
- ) |>
- dplyr::distinct()
- } else {
- df7 <- dplyr::left_join(df6, df5b) |>
- dplyr::arrange(feature_id) |>
- dplyr::mutate_all(as.character) |>
- dplyr::mutate_all(dplyr::na_if, "") |>
- dplyr::select(
- feature_id,
- component_id,
- rt,
- mz,
- molecular_formula,
- mz_error,
- library,
- smiles_2D,
- inchikey_2D,
- score_initialNormalized,
- score_biological,
- score_chemical,
- score_final,
- rank_initial,
- rank_final,
- best_candidate_organism,
- best_candidate_structure,
- consensus_structure_pat,
- consistency_structure_pat,
- consensus_structure_sup,
- consistency_structure_sup,
- consensus_structure_cla,
- consistency_structure_cla,
- reference_doi
+ df10 <- dplyr::left_join(
+ df9,
+ annotationTableWeightedChemo |>
+ dplyr::mutate_all(as.character)
+ ) |>
+ dplyr::select(dplyr::any_of(
+ c(
+ "feature_id",
+ "component_id",
+ "mz",
+ "rt",
+ "consensus_structure_pat",
+ "consistency_structure_pat",
+ "consensus_structure_sup",
+ "consistency_structure_sup",
+ "consensus_structure_cla",
+ "consistency_structure_cla"
  )
-
- df8 <- df7 |>
- dplyr::filter(!is.na(inchikey_2D))
-
- df9 <- df7 |>
- dplyr::filter(is.na(inchikey_2D))
-
- df10 <- dplyr::left_join(
- df9,
- annotationTableWeightedChemo |>
- dplyr::mutate_all(as.character)
- ) |>
- dplyr::select(
- feature_id,
- component_id,
- rt,
- mz,
- consensus_structure_pat,
- consistency_structure_pat,
- consensus_structure_sup,
- consistency_structure_sup,
- consensus_structure_cla,
- consistency_structure_cla
- ) |>
- dplyr::distinct()
- }
+ )) |>
+ dplyr::distinct()
 
  df11 <- dplyr::bind_rows(df8, df10) |>
  dplyr::arrange(as.numeric(feature_id))

diff --git a/R/process_annotations.R b/R/process_annotations.R
@@ -177,16 +177,14 @@ process_annotations <- function(library = params$library,
  col_types = "c"
  ) |>
  dplyr::filter(!is.na(structure_exact_mass)) |>
- dplyr::mutate_all(list(~ gsub(
- pattern = "\\|",
- replacement = " or ",
- x = .x
- ))) |>
- dplyr::mutate(dplyr::across(structure_exact_mass, as.numeric)) |>
- dplyr::mutate_if(is.logical, as.character)
-
- structure_organism_pairs_table[is.na(structure_organism_pairs_table)] <-
- "notClassified"
+ dplyr::mutate(dplyr::across(c(
+ "structure_exact_mass",
+ "structure_xlogp"
+ ), ~ round(as.numeric(.x), digits = 5))) |>
+ dplyr::mutate(dplyr::across(
+ tidyr::matches("taxonomy"),
+ ~ tidyr::replace_na(.x, "notClassified")
+ ))
 
  if (ms1_only == TRUE) {
  log_debug(x = "Erasing MS2 results")
@@ -282,8 +280,8 @@ process_annotations <- function(library = params$library,
 
  decorate_chemo()
 
- log_debug(x = "cleaning for cytoscape export")
- results2cytoscape <<- clean_chemo()
+ log_debug(x = "cleaning for export")
+ results <<- clean_chemo()
 
  log_debug(x = "Exporting ...")
  time <- format(Sys.time(), "%y%m%d_%H%M%OS")
@@ -297,7 +295,7 @@ process_annotations <- function(library = params$library,
  step = "process_annotations"
  )
  export_output(
- x = results2cytoscape,
+ x = results,
  file = final_output
  )
 }
diff --git a/codemeta.json b/codemeta.json
@@ -8,7 +8,7 @@
  "codeRepository": "https://github.com/taxonomicallyinformedannotation/tima-r",
  "issueTracker": "https://github.com/taxonomicallyinformedannotation/tima-r/issues",
  "license": "https://spdx.org/licenses/GPL-3.0",
- "version": "2.7.1",
+ "version": "2.7.2",
  "programmingLanguage": {
  "@type": "ComputerLanguage",
  "name": "R",
@@ -329,7 +329,7 @@
  "SystemRequirements": null
  },
  "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
- "fileSize": "2126.727KB",
+ "fileSize": "2302.216KB",
  "citation": [
  {
  "@type": "ScholarlyArticle",