Mercurial > repos > recetox > recetox_aplcms_unsupervised

annotate main.R @ 13:006736cab495 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
author recetox
date Thu, 26 May 2022 16:44:17 +0000
parents 6057540f65a9
children 202ac259e077
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d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
recetox
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1 library(recetox.aplcms)
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2 library(dplyr)
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d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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4 save_extracted_features <- function(df, filename) {
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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5 df <- as.data.frame(df)
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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6 columns <- c("mz", "pos", "sd1", "sd2", "area")
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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7 arrow::write_parquet(df[columns], filename)
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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8 }
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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10 save_aligned_feature_table <- function(df, filename) {
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11 columns <- c("feature", "mz", "rt", "sample", "sample_rt", "sample_intensity")
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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12 arrow::write_parquet(df[columns], filename)
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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13 }
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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15 save_recovered_feature_table <- function(df, filename, out_format) {
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16 columns <- c("feature", "mz", "rt", "sample", "sample_rt", "sample_intensity")
6057540f65a9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
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17 if (out_format == "recetox") {
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18 peak_table <- df[columns]
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19 recetox_peak_table <- rcx_aplcms_to_rcx_xmsannotator(peak_table)
6057540f65a9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
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20 arrow::write_parquet(recetox_peak_table, filename)
6057540f65a9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
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21 } else {
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22 arrow::write_parquet(df[columns], filename)
6057540f65a9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
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23 }
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24 }
6057540f65a9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
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26 rcx_aplcms_to_rcx_xmsannotator <- function(peak_table) {
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27 col_base <- c("feature", "mz", "rt")
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28 output_table <- peak_table %>% distinct(across(any_of(col_base)))
6057540f65a9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
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006736cab495 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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30 for (level in levels(factor(peak_table$sample))) {
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31 subdata <- peak_table %>%
6057540f65a9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
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32 filter(sample == level) %>%
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33 select(any_of(c(col_base, "sample_intensity"))) %>%
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34 rename(!!level := "sample_intensity")
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35 output_table <- inner_join(output_table, subdata, by = col_base)
6057540f65a9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
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36 }
6057540f65a9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
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37 output_table <- output_table %>% rename(peak = feature)
6057540f65a9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
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38 return(output_table)
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39 }
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41 known_table_columns <- function() {
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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42 c("chemical_formula", "HMDB_ID", "KEGG_compound_ID", "mass", "ion.type",
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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43 "m.z", "Number_profiles_processed", "Percent_found", "mz_min", "mz_max",
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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44 "RT_mean", "RT_sd", "RT_min", "RT_max", "int_mean(log)", "int_sd(log)",
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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45 "int_min(log)", "int_max(log)")
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46 }
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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48 save_known_table <- function(df, filename) {
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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49 columns <- known_table_columns()
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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50 arrow::write_parquet(df[columns], filename)
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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51 }
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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53 read_known_table <- function(filename) {
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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54 arrow::read_parquet(filename, col_select = known_table_columns())
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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55 }
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57 save_pairing <- function(df, filename) {
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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58 write.table(df, filename, row.names = FALSE, col.names = c("new", "old"))
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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59 }
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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61 save_all_extracted_features <- function(dfs, filenames) {
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62 filenames <- tools::file_path_sans_ext(basename(filenames))
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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63 filenames <- paste0(filenames, ".parquet")
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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64 filenames <- file.path("extracted", filenames)
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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65 dir.create("extracted")
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66 mapply(save_extracted_features, dfs, filenames)
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67 }
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69 save_all_corrected_features <- function(dfs, filenames) {
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70 filenames <- tools::file_path_sans_ext(basename(filenames))
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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71 filenames <- paste0(filenames, ".parquet")
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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72 filenames <- file.path("corrected", filenames)
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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73 dir.create("corrected")
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74 mapply(save_extracted_features, dfs, filenames)
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75 }
d06ec5e6721c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 831143b00343dbf66d738d5b5e7cbe9ee6f99594"
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77 unsupervised_main <- function(sample_files, aligned_file, recovered_file, out_format, ...) {
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78 sample_files <- sort_samples_by_acquisition_number(sample_files)
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80 res <- unsupervised(filenames = sample_files, ...)
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82 save_all_extracted_features(res$extracted_features, sample_files)
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83 save_all_corrected_features(res$corrected_features, sample_files)
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85 save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file)
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86 save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format)
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87 }
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89 hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, pairing_file, aligned_file, recovered_file, out_format, ...) {
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90 sample_files <- sort_samples_by_acquisition_number(sample_files)
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92 known <- read_known_table(known_table_file)
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93 res <- hybrid(filenames = sample_files, known_table = known, ...)
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95 save_known_table(res$updated_known_table, updated_known_table_file)
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96 save_pairing(res$features_known_table_pairing, pairing_file)
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98 save_all_extracted_features(res$extracted_features, sample_files)
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99 save_all_corrected_features(res$corrected_features, sample_files)
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101 save_aligned_feature_table(res$aligned_feature_sample_table, aligned_file)
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102 save_recovered_feature_table(res$recovered_feature_sample_table, recovered_file, out_format)
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103 }
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105 two_step_hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, recovered_file, aligned_file, out_format, metadata, ...) {
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106 sample_files <- sort_samples_by_acquisition_number(sample_files)
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107 metadata <- read.table(metadata, sep = ",", header = TRUE)
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109 known_table <- read_known_table(known_table_file)
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110 res <- two.step.hybrid(filenames = sample_files, known.table = known_table, work_dir = getwd(), metadata = metadata, ...)
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112 save_known_table(res$known_table, updated_known_table_file)
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113 save_aligned_feature_table(res$aligned_features, aligned_file)
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114 save_recovered_feature_table(res$final_features, recovered_file, out_format)
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115 }