Mercurial > repos > recetox > waveica

annotate waveica_wrapper.R @ 2:d08deef1eb44 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit e33ef984e78721ed37d825c6672795a539a461e1"
author recetox
date Fri, 12 Nov 2021 09:14:04 +0000
parents 2bcfd5b450bb
children 8b55efc7d117
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1 waveica <- function(data,
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2 wavelet_filter,
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3 wavelet_length,
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4 k,
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5 t,
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6 t2,
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7 alpha,
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8 exclude_blanks) {
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9
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10 # get input from the Galaxy, preprocess data
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11 data <- read.csv(data, header = TRUE)
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13 required_columns <- c("sampleName", "class", "sampleType", "injectionOrder", "batch")
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14 if (anyNA(data)) {
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15 stop("Error: dataframe cannot contain NULL values!
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16 Make sure that your dataframe does not contain empty cells")
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17 } else if (!all(required_columns %in% colnames(data))) {
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18 stop("Error: missing metadata!
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19 Make sure that the following columns are present in your dataframe: [sampleName, class, sampleType, injectionOrder, batch]")
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20 }
1
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22 # sort data by injection order
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23 data <- data[order(data[, "batch"],
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24 data[, "injectionOrder"],
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25 decreasing = FALSE
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26 ), ]
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2
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28 # separate data into features, batch and group
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29 feature_columns <- colnames(data)[!colnames(data) %in% required_columns]
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30 features <- data[, feature_columns]
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31 group <- enumerate_groups(as.character(data$sampleType))
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32 batch <- data$batch
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34 # run WaveICA
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35 features <- WaveICA::WaveICA(
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36 data = features,
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37 wf = get_wf(wavelet_filter, wavelet_length),
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38 batch = batch,
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39 group = group,
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40 K = k,
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41 t = t,
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42 t2 = t2,
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43 alpha = alpha
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44 )
0
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46 data[, feature_columns] <- features$data_wave
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48 # remove blanks from dataset
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49 if (exclude_blanks) {
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50 data <- exclude_group(data, group)
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51 }
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52
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53 return(data)
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54 }
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57 # Match group labels with [blank/sample/qc] and enumerate them
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58 enumerate_groups <- function(group) {
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59 group[grepl("blank", tolower(group))] <- 0
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60 group[grepl("sample", tolower(group))] <- 1
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61 group[grepl("qc", tolower(group))] <- 2
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63 return(group)
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64 }
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67 # Create appropriate input for R wavelets function
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68 get_wf <- function(wavelet_filter, wavelet_length) {
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69 wf <- paste(wavelet_filter, wavelet_length, sep = "")
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71 # exception to the wavelet function
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72 if (wf == "d2") {
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73 wf <- "haar"
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74 }
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76 return(wf)
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77 }
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80 # Exclude blanks from a dataframe
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81 exclude_group <- function(data, group) {
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82 row_idx_to_exclude <- which(group %in% 0)
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83 if (length(row_idx_to_exclude) > 0) {
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84 data_without_blanks <- data[-c(row_idx_to_exclude), ]
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85 cat("Blank samples have been excluded from the dataframe.\n")
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86 return(data_without_blanks)
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87 } else {
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88 return(data)
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89 }
0
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90 }
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91
2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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93 # Store output of WaveICA in a tsv file
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d08deef1eb44 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit e33ef984e78721ed37d825c6672795a539a461e1"
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94 store_data <- function(data, output) {
d08deef1eb44 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit e33ef984e78721ed37d825c6672795a539a461e1"
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95 write.table(data, file = output, sep = "\t", row.names = FALSE, quote = FALSE)
d08deef1eb44 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit e33ef984e78721ed37d825c6672795a539a461e1"
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96 cat("Normalization has been completed.\n")
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2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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97 }