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annotate NmrBucketing_script.R @ 10:06b7a5815a1c draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit e936eab761415f9337f8b4ab0ff0337e27a5b090
author lecorguille
date Fri, 21 Apr 2017 09:08:00 -0400
parents 62c62e31fc80
children
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62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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1 ################################################################################################
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2 # SPECTRA BUCKETING AND INTEGRATION FROM RAW BRUKER FILES #
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3 # User : Galaxy #
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4 # Original data : -- #
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5 # Starting date : 20-10-2014 #
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6 # Version 1 : 18-12-2014 #
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7 # Version 2 : 07-01-2015 #
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8 # Version 3 : 24-10-2016 #
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9 # #
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10 # Input files : modification on october 2016 #
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11 # - Raw bruker files included in user-defined fileName #
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12 # - Preprocessed files (alignment, ...) included in p x n dataframe #
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13 ################################################################################################
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14 NmrBucketing <- function(fileType,fileName,leftBorder = 10.0,rightBorder = 0.5,bucketSize = 0.04,exclusionZones,
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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15 exclusionZonesBorders=NULL,graph=c("None","Overlay","One_per_individual"),
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16 nomFichier,savLog.txtC = NULL)
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17 {
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18 ## Option
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19 ##---------------
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20 strAsFacL <- options()$stringsAsFactors
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21 options(stingsAsFactors = FALSE)
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22 options(warn = -1)
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25 ## Constants
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26 ##---------------
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27 topEnvC <- environment()
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28 flgC <- "\n"
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29
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30 ## Log file (in case of integration into Galaxy)
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31 ##----------------------------------------------
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32 if(!is.null(savLog.txtC))
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33 sink(savLog.txtC, append = TRUE)
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34
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35 ## Functions definition
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36 ##---------------------
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37 ## RAW BRUKER FILE READING FUNCTION
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38 NmRBrucker_read <- function(DataDir,SampleSpectrum)
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39 {
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40
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41 bruker.get_param <- function (ACQ,paramStr)
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42 {
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43 regexpStr <- paste("^...",paramStr,"=",sep="")
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44 as.numeric(gsub("^[^=]+= ","" ,ACQ[which(simplify2array(regexpr(regexpStr,ACQ))>0)]))
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45 }
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46
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47 ACQFILE <- "acqus"
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48 SPECFILE <- paste(DataDir,"/1r",sep="")
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49 PROCFILE <- paste(DataDir,"/procs",sep="")
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50
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51 ACQ <- readLines(ACQFILE)
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52 TD <- bruker.get_param(ACQ,"TD")
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53 SW <- bruker.get_param(ACQ,"SW")
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54 SWH <- bruker.get_param(ACQ,"SW_h")
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55 DTYPA <- bruker.get_param(ACQ,"DTYPA")
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56 BYTORDA <- bruker.get_param(ACQ,"BYTORDA")
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57 #ENDIAN = ifelse( BYTORDA==0, "little", "big")
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58 ENDIAN <- "little"
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59 SIZE = ifelse( DTYPA==0, 4, 8)
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60
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61 PROC <- readLines(PROCFILE)
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62 OFFSET <- bruker.get_param(PROC,"OFFSET")
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63 SI <- bruker.get_param(PROC,"SI")
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64
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65 to.read = file(SPECFILE,"rb")
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66 maxTDSI = max(TD,SI)
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67 # signal<-rev(readBin(to.read, what="int",size=SIZE, n=TD, signed = TRUE, endian = ENDIAN))
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68 signal<-rev(readBin(to.read, what="int",size=SIZE, n=maxTDSI, signed = TRUE, endian = ENDIAN))
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69 close(to.read)
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70
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71 td <- length(signal)
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72
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73 # dppm <- SW/(TD-1)
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74 dppm <- SW/(td-1)
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75 pmax <- OFFSET
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76 pmin <- OFFSET - SW
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77 ppmseq <- seq(from=pmin, to=pmax, by=dppm)
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78 signal <- 100*signal/max(signal)
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79
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80 SampleSpectrum <- cbind(ppmseq,signal)
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81 return(SampleSpectrum)
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82 }
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83
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84 ## SPECTRUM BUCKETING
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85 NmrBrucker_bucket <- function(spectrum)
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86 {
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87 # Initialisations
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88 b <- 1
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89 j <- 1
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90 # Variable number
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91 J <- round((spectrum[1,1]-spectrum[dim(spectrum)[1],1])/bucketSize)
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92 f.bucket <- matrix(rep(0,J*2),ncol=2)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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93 colnames(f.bucket) <- c("Bucket",FileNames[i])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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94
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95
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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96 # Data bucketing
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97 while (j < dim(spectrum)[1])
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98 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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99 # chemical shift
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100 BUB <- spectrum[j,1]
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101
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102 # In zone exclusion?
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103 exclusion.in <- FALSE
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104 if (!is.null(exclusionZonesBorders))
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105 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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106 for (k in 1:nrow(exclusion.zone.m))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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107 if (BUB <= exclusion.zone.m[k,1] && exclusion.zone.m[k,2] < BUB)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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108 exclusion.in <- TRUE
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109 }
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110
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111 if (exclusion.in)
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112 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
lecorguille
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113 # Bucketing
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114 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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115 BLB <- BUB - bucketSize
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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116 bucket <- spectrum[j,]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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117 while (j < dim(spectrum)[1] && spectrum[j,1] > BLB)
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118 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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119 j <- j + 1
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120 if (spectrum[j,1] > BLB)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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121 bucket <- rbind(bucket,spectrum[j,])
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122 }
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123
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124 f.bucket[b,] <- c(round(mean(bucket[,1]),3),0)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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125
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126 # Next bucket boundary
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127 BUB <- spectrum[j,1]
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128 b <- b + 1
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129 }
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130 }
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131
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132 if (!exclusion.in)
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133 # Bucketing
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134 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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135 BLB <- BUB - bucketSize
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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136 bucket <- spectrum[j,]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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137 while (j < dim(spectrum)[1] && spectrum[j,1] > BLB)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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138 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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139 j <- j + 1
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140 if (spectrum[j,1] > BLB)
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141 bucket <- rbind(bucket,spectrum[j,])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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142 }
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143
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144 # Integration (trapezoid method)
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145 s <- cumtrapz(bucket[,1],bucket[,2])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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146 f.bucket[b,] <- c(round(mean(bucket[,1]),3),abs(s[length(s)][[1]]))
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147
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148 # Next bucket boundary
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149 BUB <- spectrum[j,1]
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150 b <- b + 1
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151 }
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152 }
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153 return(f.bucket)
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154 }
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155
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156 # Exclusion zones
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157 if (!is.null(exclusionZonesBorders))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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158 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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159 exclusion.zone.m <- matrix(exclusionZonesBorders[[1]],nrow=1)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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160 if (length(exclusionZonesBorders) > 1)
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161 for (k in 2:length(exclusionZonesBorders))
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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162 exclusion.zone.m <- rbind(exclusion.zone.m,exclusionZonesBorders[[k]])
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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163 }
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164
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165 ## CHANGES
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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166 ## Inputs from zip or library (raw files)
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167 if (fileType == "zip")
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168 {
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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169 # File names
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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170 FileNames <- list.files(fileName)
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171 n <- length(FileNames)
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172
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173 # Reading and Bucketing
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174 fileName <- paste(fileName,"/",sep="")
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175
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176 i <- 1
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177 while (i <= n)
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178 {
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179 # File reading
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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180 SampleDir <- paste(fileName,FileNames[i],"/1/",sep="")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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181 setwd(SampleDir)
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182 DataDir <- "pdata/1"
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183
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184 rawSpectrum <- NmRBrucker_read(DataDir,rawSpectrum)
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185
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186 orderedSpectrum <- rawSpectrum[order(rawSpectrum[,1],decreasing=T), ]
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187
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188 # Removal of chemical shifts > leftBorder or < rightBorder boundaries
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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189 truncatedSpectrum <- orderedSpectrum[orderedSpectrum[,1] < leftBorder & orderedSpectrum[,1] > rightBorder, ]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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190 truncatedSpectrum[,1] <- round(truncatedSpectrum[,1],3)
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191
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192 # Bucketing
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193 spectrum.bucket <- NmrBrucker_bucket(truncatedSpectrum)
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194 ppm <- spectrum.bucket[,1]
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195
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196 # spectrum Concatenation
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197 if (i == 1)
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198 bucketedSpectra <- spectrum.bucket
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199 if (i > 1)
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200 bucketedSpectra <- cbind(bucketedSpectra,spectrum.bucket[,2])
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201 colnames(bucketedSpectra)[i+1] <- FileNames[i]
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202
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203 # Next sample
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204 rm(spectrum.bucket)
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205 i <- i +1
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206 }
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207 # Directory
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208 cd(fileName)
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209 }
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210
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211 ## Inputs from dataset (preprocessed files)
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212 if (fileType=="tsv")
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213 {
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214 FileNames <- colnames(fileName)
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215 n <- length(FileNames)
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216
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217 for (i in 1:ncol(fileName))
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218 {
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219 orderedSpectrum <- cbind(as.numeric(rownames(fileName)),fileName[,i])
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220 orderedSpectrum <- orderedSpectrum[order(orderedSpectrum[,1],decreasing=T), ]
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221
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222 truncatedSpectrum <- orderedSpectrum[orderedSpectrum[,1] < leftBorder & orderedSpectrum[,1] > rightBorder, ]
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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223 truncatedSpectrum[,1] <- round(truncatedSpectrum[,1],3)
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224
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225 # Bucketing
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226 spectrum.bucket <- NmrBrucker_bucket(truncatedSpectrum)
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227 ppm <- spectrum.bucket[,1]
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228
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229 # spectrum Concatenation
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230 if (i == 1)
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231 bucketedSpectra <- spectrum.bucket
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232 if (i > 1)
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233 bucketedSpectra <- cbind(bucketedSpectra,spectrum.bucket[,2])
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234 colnames(bucketedSpectra)[i+1] <- colnames(fileName)[i]
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235 }
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236 }
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237
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238 identifiants <- gsub("([- , * { } | \\[ ])","_",colnames(bucketedSpectra)[-1])
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239 colnames(bucketedSpectra) <- c(colnames(bucketedSpectra)[1],identifiants)
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240
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241 bucketedSpectra <- bucketedSpectra[bucketedSpectra[,1]!=0,]
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242 rownames(bucketedSpectra) <- paste("B",bucketedSpectra[,1],sep="")
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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243 bucketedSpectra <- bucketedSpectra[,-1]
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244
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245 # Metadata matrice outputs
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246 sampleMetadata <- data.frame(1:n)
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247 rownames(sampleMetadata) <- colnames(bucketedSpectra)
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248 colnames(sampleMetadata) <- "SampleOrder"
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249
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250 variableMetadata <- data.frame(1:nrow(bucketedSpectra))
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251 rownames(variableMetadata) <- rownames(bucketedSpectra)
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252 colnames(variableMetadata) <- "VariableOrder"
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253
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254
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255 return(list(bucketedSpectra,sampleMetadata,variableMetadata,ppm)) # ,truncatedSpectrum_matrice
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256 }
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257
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258
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259 #################################################################################################################
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260 ## Typical function call
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261 #################################################################################################################
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262 ## StudyDir <- "K:/PROJETS/Metabohub/Bruker/Tlse_BPASourisCerveau/"
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263 ## upper <- 9.5
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264 ## lower <- 0.8
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265 ## bucket.width <- 0.01
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266 ## exclusion <- TRUE
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267 ## exclusion.zone <- list(c(5.1,4.5))
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268 ## graphique <- "Overlay"
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269 ## nomFichier <- "Tlse_BPASourisCerveau_NmrBucketing_graph.pdf"
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270 ## tlse_cerveaupnd21.bucket <- NmrBucketing(StudyDir,upper,lower,bucket.width,exclusion,exclusion.zone,graphique,nomFichier)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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271 ## write.table(tlse_cerveaupnd21.bucket,file=paste(StudyDir,"Tlse_BPASourisCerveau_NmrBucketing_dataMatrix.tsv",sep=""),
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272 ## quote=FALSE,row.nmaes=FALSE,sep="\t")
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273 #################################################################################################################