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comparison isolib.R @ 6:f0fe957df1cc draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 148c6b04fff1cedd890d33e98d4fd787026a8628
author recetox
date Thu, 12 Jun 2025 09:17:20 +0000
parents 964b4559eb1b
children 06f2d0d6d107
comparison
equal deleted inserted replaced
5:964b4559eb1b 6:f0fe957df1cc
146 intensities <- append(intensities, list(patterns[[i]][, 2])) 146 intensities <- append(intensities, list(patterns[[i]][, 2]))
147 147
148 # select all columns which describe the elemental composition 148 # select all columns which describe the elemental composition
149 # remove all 12C, 35Cl etc. 149 # remove all 12C, 35Cl etc.
150 # remove isotopes which don't occur 150 # remove isotopes which don't occur
151 compositions <- as.data.frame(patterns[[i]][, -c(1, 2)]) |> 151 compositions <- as.data.frame(patterns[[i]][, -c(1, 2), drop = FALSE]) |>
152 dplyr::select(-tidyselect::any_of(monoisotopic$isotope)) |> 152 dplyr::select(-tidyselect::any_of(monoisotopic$isotope)) |>
153 dplyr::select_if(~ !all(. == 0)) 153 dplyr::select_if(~ !all(. == 0))
154 154
155 # combine elemental composition into single string 155 # combine elemental composition into single string
156 compositions <- compositions |> 156 compositions <- compositions |>
196 dplyr::rename(mz = peaks, isotopes = isos, rt = retention_time) 196 dplyr::rename(mz = peaks, isotopes = isos, rt = retention_time)
197 197
198 if (append_isotopes) { 198 if (append_isotopes) {
199 result <- result |> 199 result <- result |>
200 dplyr::mutate(result, 200 dplyr::mutate(result,
201 full_formula = paste0(formula, " (", isotopes, ")") 201 full_formula = ifelse(
202 is.na(isotopes) | isotopes == "",
203 formula,
204 paste0(formula, " (", isotopes, ")")
205 )
202 ) |> 206 ) |>
203 dplyr::select(-all_of(c("formula", "isotopes"))) |> 207 dplyr::select(-all_of(c("formula", "isotopes"))) |>
204 dplyr::rename(formula = full_formula) |> 208 dplyr::rename(formula = full_formula) |>
205 dplyr::relocate(formula, .after = name) 209 dplyr::relocate(formula, .after = name)
206 } 210 }