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@hechth
hechth committed Oct 25, 2024
1 parent cff766a commit 5c6f057
Showing 1 changed file with 124 additions and 124 deletions.
248 changes: 124 additions & 124 deletions tools/isolib/isolib.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,145 +6,145 @@ library(readr)


parse_args <- function() {
args <- commandArgs(trailingOnly = TRUE)
args <- commandArgs(trailingOnly = TRUE)

compound_table <- read_tsv(
file = args[1],
col_types = "ccd",
col_select = tidyselect::all_of(c("name", "formula")) | tidyselect::any_of("rt")
)

parsed <- list(
compound_table = compound_table,
adducts_to_use = c(unlist(strsplit(args[2], ",", fixed = TRUE))),
threshold = as.numeric(args[3]),
append_adducts = args[4],
append_isotopes = args[5],
out_format = args[6],
outfile = args[7]
)
return(parsed)
}

generate_isotope_spectra <- function(compound_table, adducts_to_use, append_adducts, threshold) {
data(isotopes)
data(adducts)

monoisotopic <- isotopes |>
dplyr::group_by(element) |>
dplyr::slice_max(abundance, n = 1) |>
dplyr::filter(!stringr::str_detect(element, "\\[|\\]"))

chemforms <- check_chemform(isotopes, compound_table$formula)[, 2]
spectra <- data.frame()

for (current in adducts_to_use) {
adduct <- adducts[adducts$Name == current, ]
multiplied_chemforms <- multiform(chemforms, adduct$Mult)

compound_table <- read_tsv(
file = args[1],
col_types = "ccd",
col_select = tidyselect::all_of(c("name", "formula")) | tidyselect::any_of("rt")
if (adduct$Ion_mode == "negative") {
merged_chemforms <- subform(multiplied_chemforms, adduct$Formula_ded)
} else {
merged_chemforms <- mergeform(multiplied_chemforms, adduct$Formula_add)
}

charge_string <- paste0(if (adduct$Charge > 0) "+" else "-", if (abs(adduct$Charge) > 1) abs(adduct$Charge) else "")
adduct_string <- paste0("[", adduct$Name, "]", charge_string)
precursor_mz <- calculateMass(multiplied_chemforms) + adduct$Mass

if (append_adducts == TRUE) {
names <- paste(compound_table$name, paste0("(", adduct$Name, ")"), sep = " ")
} else {
names <- compound_table$name
}

spectra_df <- data.frame(
name = names,
adduct = adduct_string,
formula = chemforms,
charge = adduct$Charge,
ionization_mode = adduct$Ion_mode,
precursor_mz = precursor_mz,
msLevel = as.integer(1)
)

parsed <- list(
compound_table = compound_table,
adducts_to_use = c(unlist(strsplit(args[2], ",", fixed = TRUE))),
threshold = as.numeric(args[3]),
append_adducts = args[4],
append_isotopes = args[5],
out_format=args[6],
outfile = args[7]
if ("rt" %in% colnames(compound_table)) {
spectra_df$retention_time <- compound_table$rt
}

patterns <- enviPat::isopattern(
isotopes = isotopes,
chemforms = merged_chemforms,
charge = adduct$Charge,
threshold = threshold,
)
return(parsed)
}

generate_isotope_spectra <- function(compound_table, adducts_to_use, append_adducts, threshold) {
data(isotopes)
data(adducts)

monoisotopic <- isotopes |>
dplyr::group_by(element) |>
dplyr::slice_max(abundance, n = 1) |>
dplyr::filter(!stringr::str_detect(element, "\\[|\\]"))

chemforms <- check_chemform(isotopes, compound_table$formula)[, 2]
spectra <- data.frame()

for (current in adducts_to_use) {
adduct <- adducts[adducts$Name == current, ]
multiplied_chemforms <- multiform(chemforms, adduct$Mult)

if (adduct$Ion_mode == "negative") {
merged_chemforms <- subform(multiplied_chemforms, adduct$Formula_ded)
} else {
merged_chemforms <- mergeform(multiplied_chemforms, adduct$Formula_add)
}

charge_string <- paste0(if (adduct$Charge > 0) "+" else "-", if (abs(adduct$Charge) > 1) abs(adduct$Charge) else "")
adduct_string <- paste0("[", adduct$Name, "]", charge_string)
precursor_mz <- calculateMass(multiplied_chemforms) + adduct$Mass

if (append_adducts == TRUE) {
names <- paste(compound_table$name, paste0("(", adduct$Name, ")"), sep = " ")
} else {
names <- compound_table$name
}

spectra_df <- data.frame(
name = names,
adduct = adduct_string,
formula = chemforms,
charge = adduct$Charge,
ionization_mode = adduct$Ion_mode,
precursor_mz = precursor_mz,
msLevel = as.integer(1)
)

if ("rt" %in% colnames(compound_table)) {
spectra_df$retention_time <- compound_table$rt
}

patterns <- enviPat::isopattern(
isotopes = isotopes,
chemforms = merged_chemforms,
charge = adduct$Charge,
threshold = threshold,
)

mzs <- list()
intensities <- list()
isos <- list()

for (i in seq_along(patterns)) {
mzs <- append(mzs, list(patterns[[i]][, 1]))
intensities <- append(intensities, list(patterns[[i]][, 2]))
compositions <- as.data.frame(patterns[[i]][,-c(1,2)]) |> # select all columns which describe the elemental composition
dplyr::select(-tidyselect::any_of(monoisotopic$isotope)) |> # remove all 12C, 35Cl etc.
dplyr::select_if(~ !all(. == 0)) # remove isotopes which don't occur
compositions <- compositions |>
dplyr::rowwise() |>
dplyr::mutate(isotopes = paste( # combine elemental composition into single string
purrr::map2_chr(names(compositions), dplyr::c_across(everything()), ~ paste(.x, .y, sep = ":")),
collapse = ", ")) |>
dplyr::ungroup() |>
dplyr::select(isotopes)
isos <- append(isos, list(compositions$isotopes))
}

spectra_df$mz <- mzs
spectra_df$intensity <- intensities
spectra_df$isotopes <- isos
spectra <- rbind(spectra, spectra_df)
mzs <- list()
intensities <- list()
isos <- list()

for (i in seq_along(patterns)) {
mzs <- append(mzs, list(patterns[[i]][, 1]))
intensities <- append(intensities, list(patterns[[i]][, 2]))
compositions <- as.data.frame(patterns[[i]][, -c(1, 2)]) |> # select all columns which describe the elemental composition
dplyr::select(-tidyselect::any_of(monoisotopic$isotope)) |> # remove all 12C, 35Cl etc.
dplyr::select_if(~ !all(. == 0)) # remove isotopes which don't occur
compositions <- compositions |>
dplyr::rowwise() |>
dplyr::mutate(isotopes = paste( # combine elemental composition into single string
purrr::map2_chr(names(compositions), dplyr::c_across(everything()), ~ paste(.x, .y, sep = ":")),
collapse = ", "
)) |>
dplyr::ungroup() |>
dplyr::select(isotopes)
isos <- append(isos, list(compositions$isotopes))
}
return(spectra)

spectra_df$mz <- mzs
spectra_df$intensity <- intensities
spectra_df$isotopes <- isos
spectra <- rbind(spectra, spectra_df)
}
return(spectra)
}

write_to_msp <- function(spectra, file) {
sps <- Spectra(dplyr::select(spectra, -isotopes))
export(sps, MsBackendMsp(), file = file)
sps <- Spectra(dplyr::select(spectra, -isotopes))
export(sps, MsBackendMsp(), file = file)
}

write_to_table <- function(spectra, file, append_isotopes) {
entries <- spectra |>
dplyr::rowwise() |>
dplyr::mutate(peaks = paste(unlist(mz), collapse=";"))|>
dplyr::mutate(isos = paste(unlist(isotopes), collapse=";")
)
result <- tidyr::separate_longer_delim(entries, tidyselect::all_of(c("peaks", "isos")), ";") |>
dplyr::select(-c("mz", "intensity", "isotopes")) |>
dplyr::rename(mz = peaks, isotopes=isos, rt=retention_time)

if(append_isotopes) {
result <- dplyr::mutate(result, full_formula = paste0(formula, " (", isotopes, ")")) |>
dplyr::select(-all_of(c("formula", "isotopes"))) |>
dplyr::rename(formula = full_formula) |>
dplyr::relocate(formula, .after = name)
}
readr::write_tsv(result, file=file)
entries <- spectra |>
dplyr::rowwise() |>
dplyr::mutate(peaks = paste(unlist(mz), collapse = ";")) |>
dplyr::mutate(isos = paste(unlist(isotopes), collapse = ";"))
result <- tidyr::separate_longer_delim(entries, tidyselect::all_of(c("peaks", "isos")), ";") |>
dplyr::select(-c("mz", "intensity", "isotopes")) |>
dplyr::rename(mz = peaks, isotopes = isos, rt = retention_time)

if (append_isotopes) {
result <- dplyr::mutate(result, full_formula = paste0(formula, " (", isotopes, ")")) |>
dplyr::select(-all_of(c("formula", "isotopes"))) |>
dplyr::rename(formula = full_formula) |>
dplyr::relocate(formula, .after = name)
}
readr::write_tsv(result, file = file)
}

main <- function() {
args <- parse_args()
spectra <- generate_isotope_spectra(
args$compound_table,
args$adducts_to_use,
args$append_adducts,
args$threshold
)

if(args$out_format == "msp") {
write_to_msp(spectra, args$outfile)
} else if (args$out_format == "tabular") {
write_to_table(spectra, args$outfile, args$append_isotopes)
}
args <- parse_args()
spectra <- generate_isotope_spectra(
args$compound_table,
args$adducts_to_use,
args$append_adducts,
args$threshold
)

if (args$out_format == "msp") {
write_to_msp(spectra, args$outfile)
} else if (args$out_format == "tabular") {
write_to_table(spectra, args$outfile, args$append_isotopes)
}
}

# Call the main function
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