Mercurial > repos > recetox > waveica

annotate waveica_wrapper.R @ 0:2461d20911c9 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
author recetox
date Thu, 18 Mar 2021 15:53:38 +0000
parents
children 2bcfd5b450bb
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2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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1 waveica <- function(
2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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2 data,
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3 wavelet_filter,
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4 wavelet_length,
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5 k,
2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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6 t,
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7 t2,
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8 alpha,
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9 exclude_blanks
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10 ) {
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11
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12 # get input from the Galaxy, preprocess data
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13 data <- read.csv(data, header = TRUE, row.names = "sample_name")
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14 data <- preprocess_data(data)
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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16 # remove blanks from dataset
2461d20911c9 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 91376ea7a6736351b0cc086ca1bc6c553fdcda97"
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17 if (exclude_blanks) {
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18 data <- exclude_group(data)
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19 }
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21 # separate data into features, batch and group
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22 features <- data[, -c(1:4)]
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23 group <- as.numeric(data$class)
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24 batch <- data$batch
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25
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26 # run WaveICA
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27 normalized_data <- WaveICA::WaveICA(
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28 data = features,
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29 wf = get_wf(wavelet_filter, wavelet_length),
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30 batch = batch,
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31 group = group,
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32 K = k,
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33 t = t,
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34 t2 = t2,
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35 alpha = alpha
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36 )
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38 return(normalized_data)
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39 }
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42 # Sort data, set numerical values for groups
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43 preprocess_data <- function(data) {
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44 # sort data by injection order
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45 data <- data[order(data$injectionOrder, decreasing = FALSE), ]
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47 data$class[data$class == "blank"] <- 0
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48 data$class[data$class == "sample"] <- 1
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49 data$class[data$class == "QC"] <- 2
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50
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51 return(data)
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52 }
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55 # Create appropriate input for R wavelets function
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56 get_wf <- function(wavelet_filter, wavelet_length) {
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57 wf <- paste(wavelet_filter, wavelet_length, sep = "")
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58
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59 # exception to the wavelet function
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60 if (wf == "d2") {
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61 wf <- "haar"
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62 }
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63
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64 return(wf)
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65 }
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68 # Exclude blanks from a dataframe
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69 exclude_group <- function(data) {
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70 row_idx_to_exclude <- which(data$class %in% 0)
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71 if (length(row_idx_to_exclude) > 1) {
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72 data_without_blanks <- data[-c(row_idx_to_exclude), ]
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73 msg <- paste("Blank samples have been excluded from the dataframe.\n")
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74 cat(msg)
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75 return(data_without_blanks)
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76 }
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77 else {
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78 return(data)
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79 }
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80 }
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83 # Store output of WaveICA in a tsv file
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84 store_data <- function(normalized_data, output) {
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85 write.table(normalized_data, file = output, sep = "\t", col.names = NA)
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86 cat("Normalization has been completed.\n")
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87 }