Skip to content

Commit

Permalink
fix
Browse files Browse the repository at this point in the history
  • Loading branch information
@Adafede
Adafede committed Jul 21, 2023
1 parent 8369271 commit 2e50967
Show file tree
Hide file tree
Showing 6 changed files with 133 additions and 102 deletions.
148 changes: 98 additions & 50 deletions R/harmonize_spectra.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,22 +29,22 @@ utils::globalVariables(
#'
#' @param spectra Spectra object to be harmonized
#' @param mode MS ionization mode. Must contain 'pos' or 'neg'
#' @param co_ce Name of the collision energy in mgf
#' @param co_ci Name of the compound id in mgf
#' @param co_em Name of the exact mass in mgf
#' @param co_in Name of the InChI in mgf
#' @param co_io Name of the InChI 2D in mgf
#' @param co_ik Name of the InChIKey in mgf
#' @param co_il Name of the InChIKey 2D in mgf
#' @param co_mf Name of the molecular formula in mgf
#' @param co_na Name of the name in mgf
#' @param co_po Name of the polarity in mgf
#' @param co_sm Name of the SMILES in mgf
#' @param co_sn Name of the SMILES 2D in mgf
#' @param co_si Name of the spectrum id in mgf
#' @param co_sp Name of the SPLASH in mgf
#' @param co_sy Name of the synonyms in mgf
#' @param co_xl Name of the xlogp in mgf
#' @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
#' @param col_in Name of the InChI in mgf
#' @param col_io Name of the InChI 2D in mgf
#' @param col_ik Name of the InChIKey in mgf
#' @param col_il Name of the InChIKey 2D in mgf
#' @param col_mf Name of the molecular formula in mgf
#' @param col_na Name of the name in mgf
#' @param col_po Name of the polarity in mgf
#' @param col_sm Name of the SMILES in mgf
#' @param col_sn Name of the SMILES 2D in mgf
#' @param col_si Name of the spectrum id in mgf
#' @param col_sp Name of the SPLASH in mgf
#' @param col_sy Name of the synonyms in mgf
#' @param col_xl Name of the xlogp in mgf
#'
#' @return NULL
#'
Expand All @@ -53,22 +53,70 @@ utils::globalVariables(
#' @examples NULL
harmonize_spectra <- function(spectra,
mode,
co_ce,
co_ci,
co_em,
co_in,
co_io,
co_ik,
co_il,
co_mf,
co_na,
co_po,
co_sm,
co_sn,
co_si,
co_sp,
co_sy,
co_xl) {
col_ce = get(
"col_ce",
envir = parent.frame()
),
col_ci = get(
"col_ci",
envir = parent.frame()
),
col_em = get(
"col_em",
envir = parent.frame()
),
col_in = get(
"col_in",
envir = parent.frame()
),
col_io = get(
"col_io",
envir = parent.frame()
),
col_ik = get(
"col_ik",
envir = parent.frame()
),
col_il = get(
"col_il",
envir = parent.frame()
),
col_mf = get(
"col_mf",
envir = parent.frame()
),
col_na = get(
"col_na",
envir = parent.frame()
),
col_po = get(
"col_po",
envir = parent.frame()
),
col_sm = get(
"col_sm",
envir = parent.frame()
),
col_sn = get(
"col_sn",
envir = parent.frame()
),
col_si = get(
"col_si",
envir = parent.frame()
),
col_sp = get(
"col_sp",
envir = parent.frame()
),
col_sy = get(
"col_sy",
envir = parent.frame()
),
col_xl = get(
"col_xl",
envir = parent.frame()
)) {
columns <- c(
"collision_energy",
"compound_id",
Expand All @@ -88,21 +136,21 @@ harmonize_spectra <- function(spectra,
)
columns_full <-
c(
"collision_energy" = co_ce,
"compound_id" = co_ci,
"exactmass" = co_em,
"formula" = co_mf,
"inchi" = co_in,
"inchi_2D" = co_io,
"inchikey" = co_ik,
"inchikey_2D" = co_il,
"name" = co_na,
"smiles" = co_sm,
"smiles_2D" = co_sn,
"spectrum_id" = co_si,
"splash" = co_sp,
"synonyms" = co_sy,
"xlogp" = co_xl
"collision_energy" = col_ce,
"compound_id" = col_ci,
"exactmass" = col_em,
"formula" = col_mf,
"inchi" = col_in,
"inchi_2D" = col_io,
"inchikey" = col_ik,
"inchikey_2D" = col_il,
"name" = col_na,
"smiles" = col_sm,
"smiles_2D" = col_sn,
"spectrum_id" = col_si,
"splash" = col_sp,
"synonyms" = col_sy,
"xlogp" = col_xl
)
columns_full <- columns_full[!is.na((columns_full))]
columns_missing <-
Expand All @@ -124,7 +172,7 @@ harmonize_spectra <- function(spectra,
spectra_filtered <- spectra |>
dplyr::filter(grepl(
pattern = mode,
x = !!as.name(co_po),
x = !!as.name(col_po),
ignore.case = TRUE
)) |>
dplyr::select(
Expand Down Expand Up @@ -163,6 +211,7 @@ harmonize_spectra <- function(spectra,
mz,
intensity
) |>
data.frame() |>
dplyr::mutate(
exactmass = as.numeric(exactmass),
spectrum_id = ifelse(
Expand All @@ -175,8 +224,7 @@ harmonize_spectra <- function(spectra,
yes = name,
no = compound_id
)
) |>
data.frame()
)

return(spectra_harmonized)
}
16 changes: 0 additions & 16 deletions R/prepare_libraries_spectra.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -80,22 +80,6 @@ prepare_libraries_spectra <-
spectra_harmonized <- spectra |>
extract_spectra() |>
harmonize_spectra(
co_ce = col_ce,
co_ci = col_ci,
co_em = col_em,
co_in = col_in,
co_io = col_io,
co_ik = col_ik,
co_il = col_il,
co_mf = col_mf,
co_na = col_na,
co_po = col_po,
co_sm = col_sm,
co_sn = col_sn,
co_si = col_si,
co_sp = col_sp,
co_sy = col_sy,
co_xl = col_xl,
mode = polarity
) |>
## TODO report the issue as otherwise precursorMz is lost
Expand Down
2 changes: 1 addition & 1 deletion inst/paths.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ data:
benchmark:
path: data/source/benchmark
copy: data/interim/benchmark/ALL_GNPS_210125_matchms_pubchem_cleaned_v2_copy.msp
mgf:
mgf:
neg: data/interim/benchmark/benchmark_neg.mgf
pos: data/interim/benchmark/benchmark_pos.mgf
set: data/source/benchmark/ALL_GNPS_210125_matchms_pubchem_cleaned_v2.msp
Expand Down
2 changes: 1 addition & 1 deletion inst/scripts/annotate_masses.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ log_debug(
log_debug("Authors: ", crayon::green("AR"), "\n")
log_debug("Contributors: ", crayon::blue("CH"), crayon::cyan("MS"), "\n")

targets::tar_make(names = matches("ann_ms1_pre"))
targets::tar_make(names = matches("^ann_ms1_pre"))

end <- Sys.time()

Expand Down
64 changes: 32 additions & 32 deletions man/harmonize_spectra.Rd
View file

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

3 changes: 1 addition & 2 deletions tests/testthat/test_functions.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -179,6 +179,7 @@ testthat::test_that("Whole process", {
### LOTUS
col_args <- list(
col_ce = NULL,
col_ci = "FILENAME",
col_em = "EXACTMASS",
col_in = NULL,
col_io = "INCHI",
Expand Down Expand Up @@ -211,7 +212,6 @@ testthat::test_that("Whole process", {
what = prepare_libraries_spectra,
args = c(
col_args,
col_ci = "FILENAME",
input = params$files$libraries$spectral$is$raw[[2]] |>
gsub(pattern = "lotus_pos.rds", replacement = "isdb_pos.mgf"),
output = params$files$libraries$spectral$is$pos
Expand All @@ -229,7 +229,6 @@ testthat::test_that("Whole process", {
what = prepare_libraries_spectra,
args = c(
col_args,
col_ci = "FILENAME",
input = params$files$libraries$spectral$is$raw[[1]] |>
gsub(pattern = "lotus_neg.rds", replacement = "isdb_neg.mgf"),
output = params$files$libraries$spectral$is$neg,
Expand Down

0 comments on commit 2e50967

Please sign in to comment.