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annotate wrapper_intensity_check.R @ 7:00181e66c50f draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
author workflow4metabolomics
date Wed, 09 Jul 2025 15:43:29 +0000
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7
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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1 suppressPackageStartupMessages(library(argparse))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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2
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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3 check.err <- function(err.stock) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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4 # err.stock = vector of results returned by check functions
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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5 if (length(err.stock) != 0) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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6 stop("\n- - - - - - - - -\n", err.stock, "\n- - - - - - - - -\n")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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7 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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8 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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9
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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10
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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11 # To check if the 3 standard tables match regarding identifiers
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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12 table_match <- function(dataMatrix, sampleMetadata, variableMetadata) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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13 err.stock <- character()
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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14
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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15 # Sample identifiers
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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16 dm_samples <- colnames(dataMatrix)[-1]
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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17 sm_samples <- as.character(sampleMetadata[[1]])
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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18 # Variable identifiers
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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19 dm_vars <- as.character(dataMatrix[[1]])
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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20 vm_vars <- as.character(variableMetadata[[1]])
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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21
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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22 # Check sample IDs
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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23 missing_in_sm <- setdiff(dm_samples, sm_samples)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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24 missing_in_dm <- setdiff(sm_samples, dm_samples)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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25 if (length(missing_in_sm) > 0 || length(missing_in_dm) > 0) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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26 err.stock <- c(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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27 err.stock,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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28 "\nData matrix and sample metadata do not match regarding sample identifiers."
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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29 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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30 if (length(missing_in_sm) > 0) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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31 prefix <- if (length(missing_in_sm) < 4) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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32 "\n The "
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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33 } else {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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34 "\n For example, the "
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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35 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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36 err.stock <- c(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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37 err.stock,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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38 prefix,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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39 "following identifiers found in the data matrix\n",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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40 " do not appear in the sample metadata file:\n",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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41 " ",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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42 paste(head(missing_in_sm, 3), collapse = "\n "),
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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43 "\n"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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44 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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45 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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46 if (length(missing_in_dm) > 0) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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47 prefix <- if (length(missing_in_dm) < 4) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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48 "\n The "
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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49 } else {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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50 "\n For example, the "
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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51 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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52 err.stock <- c(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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53 err.stock,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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54 prefix,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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55 "following identifiers found in the sample metadata file\n",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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56 " do not appear in the data matrix:\n",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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57 " ",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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58 paste(head(missing_in_dm, 3), collapse = "\n "),
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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59 "\n"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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60 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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61 }
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62 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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63
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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64 # Check variable IDs
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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65 missing_in_vm <- setdiff(dm_vars, vm_vars)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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66 missing_in_dm_var <- setdiff(vm_vars, dm_vars)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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67 if (length(missing_in_vm) > 0 || length(missing_in_dm_var) > 0) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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68 err.stock <- c(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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69 err.stock,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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70 "\nData matrix and variable metadata do not match regarding variable identifiers."
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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71 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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72 if (length(missing_in_vm) > 0) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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73 prefix <- if (length(missing_in_vm) < 4) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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74 "\n The "
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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75 } else {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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76 "\n For example, the "
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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77 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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78 err.stock <- c(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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79 err.stock,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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80 prefix,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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81 "following identifiers found in the data matrix\n",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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82 " do not appear in the variable metadata file:\n",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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83 " ",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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84 paste(head(missing_in_vm, 3), collapse = "\n "),
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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85 "\n"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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86 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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87 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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88 if (length(missing_in_dm_var) > 0) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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89 prefix <- if (length(missing_in_dm_var) < 4) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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90 "\n The "
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
91 } else {
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workflow4metabolomics
parents:
diff changeset
92 "\n For example, the "
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
93 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
94 err.stock <- c(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
95 err.stock,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
96 prefix,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
97 "following identifiers found in the variable metadata file\n",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
98 " do not appear in the data matrix:\n",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
99 " ",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
100 paste(head(missing_in_dm_var, 3), collapse = "\n "),
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workflow4metabolomics
parents:
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101 "\n"
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workflow4metabolomics
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diff changeset
102 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
103 }
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workflow4metabolomics
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104 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
105
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workflow4metabolomics
parents:
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106 if (length(err.stock) > 0) {
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workflow4metabolomics
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diff changeset
107 err.stock <- c(err.stock, "\nPlease check your data.\n")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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108 }
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workflow4metabolomics
parents:
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109
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workflow4metabolomics
parents:
diff changeset
110 return(err.stock)
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111 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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112
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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113
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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114 intens_check <- function(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
115 DM.name,
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workflow4metabolomics
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116 SM.name,
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workflow4metabolomics
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diff changeset
117 VM.name,
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workflow4metabolomics
parents:
diff changeset
118 method,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
119 chosen.stat,
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workflow4metabolomics
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diff changeset
120 class.col,
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workflow4metabolomics
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diff changeset
121 test.fold,
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workflow4metabolomics
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diff changeset
122 class1,
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workflow4metabolomics
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diff changeset
123 fold.frac,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
124 logarithm,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
125 VM.output,
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diff changeset
126 graphs.output) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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127 # Read input tables
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128 DM <- read.table(DM.name, header = TRUE, sep = "\t", check.names = FALSE)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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129 SM <- read.table(SM.name, header = TRUE, sep = "\t", check.names = FALSE)
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130 VM <- read.table(VM.name, header = TRUE, sep = "\t", check.names = FALSE)
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131
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132 # Table match check
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133 table.check <- table_match(DM, SM, VM)
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134 check.err(table.check)
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135
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136 # Transpose and align DM
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137 rownames(DM) <- DM[, 1]
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138 DM <- data.frame(t(DM[, -1]))
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139 DM <- merge(x = cbind(1:nrow(SM), SM), y = DM, by.x = 2, by.y = 0)
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140 DM <- DM[order(DM[, 2]), ]
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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141 rownames(DM) <- DM[, 1]
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workflow4metabolomics
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142 DM <- DM[, -c(1:(ncol(SM) + 1))]
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143
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144 stat.list <- strsplit(chosen.stat, ",")[[1]]
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145
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146 # Class assignment
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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147 if (method == "no_class") {
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workflow4metabolomics
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148 c_class <- rep("global", nrow(DM))
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149 classnames <- "global"
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150 nb_class <- 1
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151 test.fold <- "No"
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152 } else {
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153 class.col <- colnames(SM)[as.numeric(class.col)]
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workflow4metabolomics
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154 if (!(class.col %in% colnames(SM))) {
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workflow4metabolomics
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155 stop("The column ", class.col, " is not in sample metadata")
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156 }
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157 c_class <- as.factor(SM[, class.col])
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158 nb_class <- nlevels(c_class)
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159 classnames <- levels(c_class)
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workflow4metabolomics
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160 if (nb_class < 2 && test.fold == "Yes") {
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workflow4metabolomics
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diff changeset
161 cat(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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diff changeset
162 "The '",
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diff changeset
163 class.col,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
164 "' column contains only one class, fold calculation could not be executed.\n"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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165 )
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166 }
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167 if (nb_class > (nrow(SM)) / 3 && method == "each_class") {
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168 cat("There are too many classes, consider reducing the number.\n")
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workflow4metabolomics
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169 }
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170 if (method == "one_class") {
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workflow4metabolomics
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171 if (!(class1 %in% classnames)) {
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workflow4metabolomics
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172 stop("The '", class1, "' class does not appear in the '", class.col, "'column.")
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173 }
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174 c_class <- factor(
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workflow4metabolomics
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175 ifelse(c_class == class1, class1, "Other"),
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176 levels = c(class1, "Other")
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workflow4metabolomics
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177 )
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workflow4metabolomics
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178 nb_class <- nlevels(c_class)
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179 classnames <- levels(c_class)
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180 }
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workflow4metabolomics
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181 }
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182
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183 # Check numeric
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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184 if (!is.numeric(as.matrix(DM))) {
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workflow4metabolomics
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185 findchar <- function(myval) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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186 ifelse(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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187 is.na(myval),
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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188 "ok",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
189 ifelse(is.na(as.numeric(as.character(myval))), "char", "ok")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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190 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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191 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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192 chardiag <- suppressWarnings(apply(DM, 2, vapply, findchar, "character"))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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193 charlist <- which(chardiag == "char")
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workflow4metabolomics
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194 err.stock <- paste(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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195 "\n- - - - - - - - -\nYour dataMatrix contains",
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workflow4metabolomics
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196 length(charlist),
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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197 "non-numeric value(s).\n"
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workflow4metabolomics
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198 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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199 stop(c(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
200 err.stock,
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workflow4metabolomics
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201 "The dataMatrix file is supposed to contain only numeric values.\n- - - - - - - - -\n"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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202 ))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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203 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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204
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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205 DM <- cbind(c_class, DM)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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206 stat.res <- t(DM[0, -1, drop = FALSE])
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workflow4metabolomics
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207 names <- NULL
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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208
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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209 mean.res <- sd.res <- med.res <- quart.res <- dec.res <- NA.res <- pct_NA.res <- fold.res <- NULL
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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210 mean.names <- sd.names <- med.names <- quart.names <- dec.names <- NA.names <- pct_NA.names <- fold.names <- NULL
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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211 graphs <- if (("NA" %in% stat.list) || (test.fold == "Yes")) 1 else 0
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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212 data_bp <- data.frame()
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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213
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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214 for (j in 1:nb_class) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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215 idx <- which(DM$c_class == classnames[j])
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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216 # Mean
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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217 if ("mean" %in% stat.list) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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218 mean.res <- cbind(mean.res, colMeans(DM[idx, -1], na.rm = TRUE))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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219 mean.names <- cbind(mean.names, paste("Mean", classnames[j], sep = "_"))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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220 if (j == nb_class) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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221 stat.res <- cbind(stat.res, mean.res)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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222 names <- cbind(names, mean.names)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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223 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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224 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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diff changeset
225 # SD
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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226 if ("sd" %in% stat.list) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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227 sd.res <- cbind(sd.res, apply(DM[idx, -1], 2, sd, na.rm = TRUE))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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228 sd.names <- cbind(sd.names, paste("Sd", classnames[j], sep = "_"))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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229 if (j == nb_class) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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230 stat.res <- cbind(stat.res, sd.res)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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231 names <- cbind(names, sd.names)
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232 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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233 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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234 # Median
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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235 if (("median" %in% stat.list) && (!("quartile" %in% stat.list))) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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236 med.res <- cbind(med.res, apply(DM[idx, -1], 2, median, na.rm = TRUE))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
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237 med.names <- cbind(med.names, paste("Median", classnames[j], sep = "_"))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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238 if (j == nb_class) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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239 stat.res <- cbind(stat.res, med.res)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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240 names <- cbind(names, med.names)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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241 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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242 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
243 # Quartiles
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
244 if ("quartile" %in% stat.list) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
245 quart.res <- cbind(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
246 quart.res,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
247 t(apply(DM[idx, -1], 2, quantile, na.rm = TRUE))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
248 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
249 quart.names <- cbind(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
250 quart.names,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
251 paste("Min", classnames[j], sep = "_"),
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
252 paste("Q1", classnames[j], sep = "_"),
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
253 paste("Median", classnames[j], sep = "_"),
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
254 paste("Q3", classnames[j], sep = "_"),
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
255 paste("Max", classnames[j], sep = "_")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
256 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
257 if (j == nb_class) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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258 stat.res <- cbind(stat.res, quart.res)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
259 names <- cbind(names, quart.names)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
260 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
261 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
262 # Deciles
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
263 if ("decile" %in% stat.list) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
264 dec.res <- cbind(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
265 dec.res,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
266 t(apply(DM[idx, -1], 2, quantile, na.rm = TRUE, seq(0, 1, 0.1)))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
267 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
268 dec.names <- cbind(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
269 dec.names,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
270 t(matrix(paste("D", seq(0, 10, 1), sep = "_", classnames[j])))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
271 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
272 if (j == nb_class) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
273 stat.res <- cbind(stat.res, dec.res)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
274 names <- cbind(names, dec.names)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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275 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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276 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
277 # Missing values
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
278 if ("NA" %in% stat.list) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
279 nb_NA <- apply(DM[idx, -1], 2, function(x) sum(is.na(x)))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
280 pct_NA <- round(nb_NA / nrow(DM[idx, -1]) * 100, 4)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
281 NA.res <- cbind(NA.res, nb_NA)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
282 pct_NA.res <- cbind(pct_NA.res, pct_NA)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
283 NA.names <- cbind(NA.names, paste("NA", classnames[j], sep = "_"))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
284 pct_NA.names <- cbind(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
285 pct_NA.names,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
286 paste("Pct_NA", classnames[j], sep = "_")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
287 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
288 if (j == nb_class) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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289 stat.res <- cbind(stat.res, NA.res, pct_NA.res)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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290 names <- cbind(names, NA.names, pct_NA.names)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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291 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
292 # Barplot data
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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293 bins <- cut(pct_NA, breaks = c(-1, 20, 40, 60, 80, 100), labels = FALSE)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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294 for (b in 1:5) data_bp[b, j] <- sum(bins == b)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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295 rownames(data_bp) <- c(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
296 "0%-20%",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
297 "20%-40%",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
298 "40%-60%",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
299 "60%-80%",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
300 "80%-100%"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
301 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
302 if (j == nb_class) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
303 if (sum(NA.res) == 0) cat("Data Matrix contains no NA.\n")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
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304 colnames(data_bp) <- classnames
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
305 data_bp <- as.matrix(data_bp)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
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diff changeset
306 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
307 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
308 # Mean fold change
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
309 if (test.fold == "Yes" && nb_class >= 2 && j != nb_class) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
310 if (method == "each_class") fold.frac <- "Top"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
311 for (k in (j + 1):nb_class) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
312 ratio1 <- if (fold.frac == "Bottom") classnames[k] else classnames[j]
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
313 ratio2 <- if (fold.frac == "Bottom") classnames[j] else classnames[k]
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
314 fold <- colMeans(DM[which(DM$c_class == ratio1), -1], na.rm = TRUE) /
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
315 colMeans(DM[which(DM$c_class == ratio2), -1], na.rm = TRUE)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
316 if (logarithm == "log2") {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
317 fold <- log2(fold)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
318 } else if (
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
319 logarithm == "log10"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
320 ) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
321 fold <- log10(fold)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
322 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
323 fold.res <- cbind(fold.res, fold)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
324 fname <- if (logarithm == "none") {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
325 paste("fold", ratio1, "VS", ratio2, sep = "_")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
326 } else {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
327 paste(logarithm, "fold", ratio1, "VS", ratio2, sep = "_")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
328 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
329 fold.names <- cbind(fold.names, fname)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
330 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
331 if (j == nb_class) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
332 stat.res <- cbind(stat.res, fold.res)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
333 names <- cbind(names, fold.names)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
334 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
335 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
336 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
337
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
338 # Ensure unique column names
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
339 VM.names <- colnames(VM)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
340 for (i in seq_along(VM.names)) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
341 for (j in seq_along(names)) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
342 if (VM.names[i] == names[j]) names[j] <- paste(names[j], "2", sep = "_")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
343 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
344 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
345 colnames(stat.res) <- names
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
346
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
347 # Output
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
348 VM <- cbind(VM, stat.res)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
349 write.table(VM, VM.output, sep = "\t", quote = FALSE, row.names = FALSE)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
350
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
351 # Graphics
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
352 pdf(graphs.output)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
353 if (graphs == 1) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
354 if ("NA" %in% stat.list) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
355 graph.colors <- c("green3", "palegreen3", "lightblue", "orangered", "red")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
356 par(mar = c(5.1, 4.1, 4.1, 8.1), xpd = TRUE)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
357 bp <- barplot(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
358 data_bp,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
359 col = graph.colors,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
360 main = "Proportion of NA",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
361 xlab = "Classes",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
362 ylab = "Variables"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
363 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
364 legend(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
365 "topright",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
366 fill = graph.colors,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
367 rownames(data_bp),
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
368 inset = c(-0.3, 0)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
369 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
370 stock <- 0
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
371 for (i in 1:nrow(data_bp)) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
372 text(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
373 bp,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
374 stock + data_bp[i, ] / 2,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
375 data_bp[i, ],
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
376 col = "white",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
377 cex = 0.7
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
378 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
379 stock <- stock + data_bp[i, ]
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
380 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
381 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
382 if ((test.fold == "Yes") && (nb_class >= 2)) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
383 clean_fold <- fold.res
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
384 clean_fold[is.infinite(clean_fold)] <- NA
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
385 for (j in 1:ncol(clean_fold)) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
386 boxplot(clean_fold[, j], main = fold.names[j])
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
387 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
388 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
389 } else {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
390 plot.new()
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
391 legend("center", "You did not select any option with graphical output.")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
392 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
393 dev.off()
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
394 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
395
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
396
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
397 parser <- ArgumentParser(description = "Intensity Check Tool")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
398
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
399 parser$add_argument(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
400 "--dataMatrix_in",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
401 required = TRUE,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
402 help = "Input data matrix file"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
403 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
404 parser$add_argument(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
405 "--sampleMetadata_in",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
406 required = TRUE,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
407 help = "Input sample metadata file"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
408 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
409 parser$add_argument(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
410 "--variableMetadata_in",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
411 required = TRUE,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
412 help = "Input variable metadata file"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
413 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
414 parser$add_argument("--method", required = TRUE, help = "Computation method")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
415 parser$add_argument(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
416 "--chosen_stat",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
417 required = TRUE,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
418 help = "Statistics to compute"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
419 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
420 parser$add_argument(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
421 "--class_col",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
422 default = NULL,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
423 help = "Class column (optional)"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
424 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
425 parser$add_argument(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
426 "--test_fold",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
427 default = NULL,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
428 help = "Test fold (optional)"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
429 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
430 parser$add_argument("--class1", default = NULL, help = "Class1 (optional)")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
431 parser$add_argument(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
432 "--fold_frac",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
433 default = NULL,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
434 help = "Fold fraction (optional)"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
435 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
436 parser$add_argument(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
437 "--logarithm",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
438 default = NULL,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
439 help = "Logarithm (optional)"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
440 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
441 parser$add_argument(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
442 "--variableMetadata_out",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
443 required = TRUE,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
444 help = "Output variable metadata file"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
445 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
446 parser$add_argument(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
447 "--graphs_out",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
448 required = TRUE,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
449 help = "Output graphs file"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
450 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
451
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
452 args <- parser$parse_args()
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
453
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
454 print(args)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
455
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
456 if (length(args) < 7) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
457 stop("NOT enough argument !!!")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
458 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
459
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
460 cat(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
461 "\nJob starting time:\n",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
462 format(Sys.time(), "%a %d %b %Y %X"),
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
463 "\n\n--------------------------------------------------------------------",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
464 "\nIntensity Check parameters:\n\n"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
465 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
466 print(args)
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
467 cat("--------------------------------------------------------------------\n\n")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
468
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
469 class_col <- NULL
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
470 test_fold <- NULL
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
471 class1 <- NULL
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
472 fold_frac <- NULL
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
473 logarithm <- NULL
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
474 if (args$method == "each_class") {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
475 class_col <- args$class_col
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
476 test_fold <- args$test_fold
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
477 if (args$test_fold == "Yes") {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
478 logarithm <- args$logarithm
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
479 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
480 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
481 if (args$method == "one_class") {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
482 class_col <- args$class_col
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
483 class1 <- args$class1
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
484 test_fold <- args$test_fold
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
485 if (args$test_fold == "Yes") {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
486 fold_frac <- args$fold_frac
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
487 logarithm <- args$logarithm
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
488 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
489 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
490
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
491 err_no_option <- NULL
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
492
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
493 if (
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
494 ((args$method == "no_class") && (args$chosen_stat == "None")) ||
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
495 ((args$method != "no_class") &&
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
496 (args$chosen_stat == "None") &&
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
497 (test_fold == "No"))
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
498 ) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
499 err_no_option <- "You did not select any computational option. Program can not be executed."
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
500 stop("\n- - - - - - - - -\n", err_no_option, "\n- - - - - - - - -\n")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
501 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
502
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
503
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
504 if (is.null(err_no_option)) {
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
505 intens_check(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
506 args$dataMatrix_in,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
507 args$sampleMetadata_in,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
508 args$variableMetadata_in,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
509 args$method,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
510 args$chosen_stat,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
511 class_col,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
512 test_fold,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
513 class1,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
514 fold_frac,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
515 logarithm,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
516 args$variableMetadata_out,
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
517 args$graphs_out
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
518 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
519 }
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
520
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
521
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
522 cat(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
523 "\n--------------------------------------------------------------------",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
524 "\nInformation about R (version, Operating System, attached or loaded packages):\n\n"
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
525 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
526 sessionInfo()
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
527 cat(
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
528 "--------------------------------------------------------------------\n",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
529 "\nJob ending time:\n",
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
530 format(Sys.time(), "%a %d %b %Y %X")
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
531 )
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
532
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
533
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
534 # delete the parameters to avoid the passage to the next tool in .RData image
00181e66c50f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 689ab2a3db06eeed6a190f3cfa1618b9d9b7b07b
workflow4metabolomics
parents:
diff changeset
535 rm(args)