Mercurial > repos > recetox > test_recetox_aplcms_unsupervised

comparison main.R @ 0:be51059c2384 draft default tip

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 65d42862f9265e8ba3783368ac0bddb154e3a427-dirty"
author recetox
date Fri, 18 Jun 2021 16:36:23 +0000
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-1:000000000000 0:be51059c2384
1 library(recetox.aplcms)
2
3 save_extracted_features <- function(df, filename) {
4 df <- as.data.frame(df)
5 columns <- c("mz", "pos", "sd1", "sd2", "area")
6 arrow::write_parquet(df[columns], filename)
7 }
8
9 save_feature_sample_table <- function(df, filename) {
10 columns <- c("feature", "mz", "rt", "sample", "sample_rt", "sample_intensity")
11 arrow::write_parquet(df[columns], filename)
12 }
13
14 known_table_columns <- function() {
15 c("chemical_formula", "HMDB_ID", "KEGG_compound_ID", "mass", "ion.type",
16 "m.z", "Number_profiles_processed", "Percent_found", "mz_min", "mz_max",
17 "RT_mean", "RT_sd", "RT_min", "RT_max", "int_mean(log)", "int_sd(log)",
18 "int_min(log)", "int_max(log)")
19 }
20
21 save_known_table <- function(df, filename) {
22 columns <- known_table_columns()
23 arrow::write_parquet(df[columns], filename)
24 }
25
26 read_known_table <- function(filename) {
27 arrow::read_parquet(filename, col_select = known_table_columns())
28 }
29
30 save_pairing <- function(df, filename) {
31 write.table(df, filename, row.names = FALSE, col.names = c("new", "old"))
32 }
33
34 save_all_extracted_features <- function(dfs, filenames) {
35 filenames <- tools::file_path_sans_ext(basename(filenames))
36 filenames <- paste0(filenames, ".parquet")
37 filenames <- file.path("extracted", filenames)
38 dir.create("extracted")
39 mapply(save_extracted_features, dfs, filenames)
40 }
41
42 save_all_corrected_features <- function(dfs, filenames) {
43 filenames <- tools::file_path_sans_ext(basename(filenames))
44 filenames <- paste0(filenames, ".parquet")
45 filenames <- file.path("corrected", filenames)
46 dir.create("corrected")
47 mapply(save_extracted_features, dfs, filenames)
48 }
49
50 unsupervised_main <- function(sample_files, aligned_file, recovered_file, ...) {
51 sample_files <- sort_samples_by_acquisition_number(sample_files)
52
53 res <- unsupervised(filenames = sample_files, ...)
54
55 save_all_extracted_features(res$extracted_features, sample_files)
56 save_all_corrected_features(res$corrected_features, sample_files)
57
58 save_feature_sample_table(res$aligned_feature_sample_table, aligned_file)
59 save_feature_sample_table(res$recovered_feature_sample_table, recovered_file)
60 }
61
62 hybrid_main <- function(sample_files, known_table_file, updated_known_table_file, pairing_file, aligned_file, recovered_file, ...) {
63 sample_files <- sort_samples_by_acquisition_number(sample_files)
64
65 known <- read_known_table(known_table_file)
66 res <- hybrid(filenames = sample_files, known_table = known, ...)
67
68 save_known_table(res$updated_known_table, updated_known_table_file)
69 save_pairing(res$features_known_table_pairing, pairing_file)
70
71 save_all_extracted_features(res$extracted_features, sample_files)
72 save_all_corrected_features(res$corrected_features, sample_files)
73
74 save_feature_sample_table(res$aligned_feature_sample_table, aligned_file)
75 save_feature_sample_table(res$recovered_feature_sample_table, recovered_file)
76 }