Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing

annotate NmrBucketing_wrapper.R @ 9:62c62e31fc80 draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
author lecorguille
date Fri, 21 Apr 2017 08:53:40 -0400
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9
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
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2
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3 ## 070115_NmrBucketing2galaxy_v1.R
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4 ## Marie Tremblay-Franco
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5 ## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics
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6 ## www.metabohub.fr/en
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7 ## marie.tremblay-franco@toulouse.inra.fr
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8
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9 runExampleL <- FALSE
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10
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11 if(runExampleL) {
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12 ##------------------------------
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13 ## Example of arguments
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14 ##------------------------------
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15 argLs <- list(StudyDir = "Tlse_BPASourisCerveau",
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16 upper = "10.0",
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17 lower = "0.50",
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18 bucket.width = "0.01",
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19 exclusion = "TRUE",
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20 exclusion.zone = list(c(6.5,4.5)),
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21 graph="Overlay")
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23 argLs <- c(argLs,
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24 list(dataMatrixOut = paste(directory,"_NmrBucketing_dataMatrix.tsv",sep=""),
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25 sampleMetadataOut = paste(directory,"_NmrBucketing_sampleMetadata.tsv",sep=""),
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26 variableMetadataOut = paste(directory,"_NmrBucketing_variableMetadata.tsv",sep=""),
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27 graphOut = paste(directory,"_NmrBucketing_graph.pdf",sep=""),
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28 logOut = paste(directory,"_NmrBucketing_log.txt",sep="")))
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29 }
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31 ##------------------------------
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32 ## Options
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33 ##------------------------------
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34 strAsFacL <- options()$stringsAsFactors
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35 options(stringsAsFactors = FALSE)
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36
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37
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38 ##------------------------------
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39 ## Libraries laoding
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40 ##------------------------------
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41 # For parseCommandArgs function
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42 library(batch)
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43 # For cumtrapz function
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44 library(pracma)
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45
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46 # R script call
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47 source_local <- function(fname)
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48 {
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49 argv <- commandArgs(trailingOnly = FALSE)
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50 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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51 source(paste(base_dir, fname, sep="/"))
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52 }
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53 #Import the different functions
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54 source_local("NmrBucketing_script.R")
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55 source_local("DrawSpec.R")
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56
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57 ##------------------------------
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58 ## Errors ?????????????????????
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59 ##------------------------------
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61
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62 ##------------------------------
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63 ## Constants
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64 ##------------------------------
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65 topEnvC <- environment()
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66 flagC <- "\n"
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68
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69 ##------------------------------
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70 ## Script
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71 ##------------------------------
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72 if(!runExampleL)
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73 argLs <- parseCommandArgs(evaluate=FALSE)
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74
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75
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76 ## Parameters Loading
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77 ##-------------------
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78 # Inputs
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79 if (!is.null(argLs[["zipfile"]])){
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80 fileType="zip"
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81 zipfile= argLs[["zipfile"]]
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82 directory=unzip(zipfile, list=F)
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83 directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")
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84 } else if (!is.null(argLs[["tsvfile"]])){
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85 fileType="tsv"
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86 directory <- read.table(argLs[["tsvfile"]],check.names=FALSE,header=TRUE,sep="\t")
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87 }
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88
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89 leftBorder <- argLs[["left_border"]]
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90 rightBorder <- argLs[["right_border"]]
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91 bucketSize <- argLs[["bucket_width"]]
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92 exclusionZones <- argLs[["zone_exclusion_choices.choice"]]
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93
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
94 exclusionZonesBorders <- NULL
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
95 if (!is.null(argLs$zone_exclusion_left))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
96 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
97 for(i in which(names(argLs)=="zone_exclusion_left"))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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98 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
99 exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]])))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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100 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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101 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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102
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lecorguille
parents:
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103 graphique <- argLs[["graphType"]]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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104
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lecorguille
parents:
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105 # Outputs
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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106 nomGraphe <- argLs[["graphOut"]]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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107 dataMatrixOut <- argLs[["dataMatrixOut"]]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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108 logFile <- argLs[["logOut"]]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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109 if (fileType=="zip")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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110 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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111 sampleMetadataOut <- argLs[["sampleOut"]]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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112 variableMetadataOut <- argLs[["variableOut"]]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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113 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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114
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lecorguille
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115 ## Checking arguments
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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116 ##-------------------
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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117 error.stock <- "\n"
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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118
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lecorguille
parents:
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119 if(length(error.stock) > 1)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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120 stop(error.stock)
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lecorguille
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121
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122
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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123 ## Computation
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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124 ##------------
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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125 outputs <- NmrBucketing(fileType=fileType, fileName=directory, leftBorder=leftBorder, rightBorder=rightBorder, bucketSize=bucketSize,
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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126 exclusionZones=exclusionZones, exclusionZonesBorders=exclusionZonesBorders, graph=graphique, nomFichier=nomGraphe,
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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127 savLog.txtC=logFile)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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128 data_bucket <- outputs[[1]]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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129 data_sample <- outputs[[2]]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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130 data_variable <- outputs[[3]]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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131 ppm <- outputs[[4]]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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132 ppm <- round(ppm,2)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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133
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134 ## Graphical outputs
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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135 ##------------------
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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136 if (graphique != "None")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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137 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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138 excludedZone <- NULL
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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139 for (c in 1:length(exclusionZonesBorders))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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140 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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141 excludedZone <- c(excludedZone,exclusionZonesBorders[[c]])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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142 excludedZone <- sort(excludedZone)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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143 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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144 nbZones <- length(excludedZone)/2
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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145 n <- length(excludedZone)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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146
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lecorguille
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147 # Graphic Device opening
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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148 pdf(nomGraphe,onefile=TRUE)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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149
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150 if (graphique == "Overlay")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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151 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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152 # Global spectral window
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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153 spectra <- data.frame(t(data_bucket))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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154 drawSpec(spectra,xlab="", ylab="Intensity", main="")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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155
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lecorguille
parents:
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156 ## Zoomed spectral window depending on exclusion zone(s)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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157 if (nbZones != 0)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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158 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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159 BInf <- excludedZone[n]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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160 if (round(BInf,1) == BInf)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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161 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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parents:
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162 BInf <- BInf+0.01
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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163 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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164 spectra <- data.frame(t(data_bucket[1:(which(ppm == BInf)[[1]]),]))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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165 drawSpec(spectra,xlab="", ylab="Intensity", main="")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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166 n <- n - 1
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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167
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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168 while (n >= nbZones & nbZones > 1)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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169 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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170 BInf <- excludedZone[n-1]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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171 if (round(BInf,1) > BInf)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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172 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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173 BInf <- BInf+0.01
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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174 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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parents:
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175 spectra <- data.frame(t(data_bucket[(which(ppm == excludedZone[n])[[1]]):(which(ppm == BInf)[[1]]),]))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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176 drawSpec(spectra,xlab="", ylab="Intensity", main="")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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177 n <- n - 2
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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178 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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179
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180 BInf <- excludedZone[1]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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181 if (round(BInf,1) <= BInf)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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182 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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183 BInf <- BInf+0.01
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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184 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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185 spectra <- data.frame(t(data_bucket[(which(ppm == BInf)[[1]]):nrow(data_bucket),]))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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186 drawSpec(spectra,xlab="", ylab="Intensity", main="")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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187 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
188 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
189 else
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
190 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
191 for (i in 1:ncol(data_bucket))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
192 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
193 par(mfrow=c((nbZones+2),1))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
194 n <- length(excludedZone)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
195 spectra <- t(data_bucket[,i])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
196 names(spectra) <- rownames(data_bucket)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
197 plot(1:length(spectra), spectra, type='l', xlab="", ylab="Intensity", main=colnames(data_bucket)[i], xaxt = "n")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
198 xPos <- 1
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
199 nAxisPos <- 4
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
200 startP <- length(nAxisPos)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
201 endP <- nrow(data_bucket)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
202 GraphRange <- c(startP:endP)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
203 tempVal = trunc(length(GraphRange)/nAxisPos)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
204 xPos = c(0:nAxisPos) * tempVal
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
205 axis(1, at = xPos, labels = rownames(data_bucket)[xPos + startP])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
206
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
207 ## Zoomed spectral window depending on exclusion zone(s)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
208 if (nbZones != 0)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
209 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
210 BInf <- excludedZone[n]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
211 if (round(BInf,1) == BInf)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
212 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
213 BInf <- BInf+0.01
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
214 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
215 spectra <- t(data_bucket[1:(which(ppm == BInf)[[1]]),i])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
216 names(spectra) <- rownames(data_bucket)[1:(which(ppm == BInf)[[1]])]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
217 plot(1:length(spectra), spectra, type='l',xlab="", ylab="Intensity", main="", xaxt = "n")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
218 xPos <- 1
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
219 nAxisPos <- 4
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
220 startP <- length(nAxisPos)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
221 endP <- length(spectra)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
222 GraphRange <- c(startP:endP)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
223 tempVal = trunc(length(GraphRange)/nAxisPos)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
224 xPos = c(0:nAxisPos) * tempVal
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
225 axis(1, at = xPos, labels = rownames(data_bucket)[xPos + startP])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
226 n <- n - 1
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
227
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
228 while (n >= nbZones & nbZones > 1)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
229 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
230 BInf <- excludedZone[n-1]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
231 if (round(BInf,1) > BInf)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
232 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
233 BInf <- BInf+0.01
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
234 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
235 spectra <- t(data_bucket[(which(ppm == excludedZone[n])[[1]]):(which(ppm == BInf)[[1]]),i])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
236 names(spectra) <- rownames(data_bucket)[(which(ppm == excludedZone[n])[[1]]):(which(ppm == BInf)[[1]])]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
237 plot(1:length(spectra), spectra, type='l',xlab="", ylab="Intensity", main="", xaxt = "n")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
238 xPos <- 1
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
239 nAxisPos <- 4
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
240 startP <- length(nAxisPos)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
241 endP <- length(spectra)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
242 GraphRange <- c(startP:endP)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
243 tempVal = trunc(length(GraphRange)/nAxisPos)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
244 xPos = c(0:nAxisPos) * tempVal
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
245 axis(1, at = xPos, labels = rownames(data_bucket)[xPos + startP])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
246 n <- n - 2
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
247 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
248
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
249 BInf <- excludedZone[1]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
250 if (round(BInf,1) <= BInf)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
251 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
252 BInf <- BInf+0.01
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
253 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
254 spectra <- t(data_bucket[(which(ppm == BInf)[[1]]):nrow(data_bucket),i])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
255 names(spectra) <- rownames(data_bucket)[(which(ppm == BInf)[[1]]):nrow(data_bucket)]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
256 plot(1:length(spectra), spectra, type='l',xlab="", ylab="Intensity", main="", xaxt = "n")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
257 xPos <- 1
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
258 nAxisPos <- 4
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
259 startP <- length(nAxisPos)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
260 endP <- length(spectra)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
261 GraphRange <- c(startP:endP)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
262 tempVal = trunc(length(GraphRange)/nAxisPos)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
263 xPos = c(0:nAxisPos) * tempVal
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
264 axis(1, at = xPos, labels = rownames(data_bucket)[xPos + startP])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
265 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
266 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
267 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
268 dev.off()
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
269 }
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
270 ## Saving
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
271 ##-------
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
272 # Data
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
273 data_bucket <- cbind(rownames(data_bucket),data_bucket)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
274 colnames(data_bucket) <- c("Bucket",colnames(data_bucket)[-1])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
275 write.table(data_bucket,file=argLs$dataMatrixOut,quote=FALSE,row.names=FALSE,sep="\t")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
276 # Sample
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
277 data_sample <- cbind(rownames(data_sample),data_sample)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
diff changeset
278 colnames(data_sample) <- c("Sample",colnames(data_sample)[-1])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
parents:
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279 write.table(data_sample,file=argLs$sampleOut,quote=FALSE,row.names=FALSE,sep="\t")
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280 # Variable
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281 data_variable <- cbind(rownames(data_variable),data_variable)
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282 colnames(data_variable) <- c("Bucket",colnames(data_variable)[-1])
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283 write.table(data_variable,file=argLs$variableOut,quote=FALSE,row.names=FALSE,sep="\t")
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284
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285
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286 ## Ending
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287 ##---------------------
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288
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289 cat("\nEnd of 'NMR bucketing' Galaxy module call: ", as.character(Sys.time()), sep = "")
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290
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291 ## sink(NULL)
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292
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293 options(stringsAsFactors = strAsFacL)
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294
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295 rm(list = ls())