Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing

annotate NmrBucketing_script.R @ 3:58679e85745f draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 7cd224b2cbddcb2535640a3f76194bd235acb602-dirty
author lecorguille
date Fri, 12 Aug 2016 05:47:27 -0400
parents 761312f27add
children d61f6ceef5d6
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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1 ################################################################################################
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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2 # SPECTRA BUCKETING AND INTEGRATION FROM RAW BRUKER FILES #
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3 # User : Galaxy #
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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4 # Original data : -- #
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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5 # Starting date : 20-10-2014 #
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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6 # Version 1 : 18-12-2014 #
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7 # Version 2 : 07-01-2015 #
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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8 # #
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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9 # Input files : files in included in user-defined directory #
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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10 ################################################################################################
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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11 NmrBucketing <- function(directory,leftBorder = 10.0,rightBorder = 0.5,bucketSize = 0.04,exclusionZones,exclusionZonesBorders=NULL,
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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12 graph=c("None","Overlay","One_per_individual"),nomFichier,savLog.txtC = NULL)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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13 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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14 ## Option
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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15 ##---------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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16 strAsFacL <- options()$stringsAsFactors
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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17 options(stingsAsFactors = FALSE)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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18 options(warn = -1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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21 ## Constants
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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22 ##---------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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23 topEnvC <- environment()
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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24 flgC <- "\n"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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26 ## Log file (in case of integration into Galaxy)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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27 ##----------------------------------------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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28 if(!is.null(savLog.txtC))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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29 sink(savLog.txtC, append = TRUE)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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31 ## Functions definition
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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32 ##---------------------
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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33 ## RAW BRUKER FILE READING FUNCTION
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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34 NmRBrucker_read <- function(DataDir,SampleSpectrum)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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35 {
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36
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37 bruker.get_param <- function (ACQ,paramStr)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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38 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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39 regexpStr <- paste("^...",paramStr,"=",sep="")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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40 as.numeric(gsub("^[^=]+= ","" ,ACQ[which(simplify2array(regexpr(regexpStr,ACQ))>0)]))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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41 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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42
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43 ACQFILE <- "acqus"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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44 SPECFILE <- paste(DataDir,"/1r",sep="")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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45 PROCFILE <- paste(DataDir,"/procs",sep="")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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46
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47 ACQ <- readLines(ACQFILE)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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48 TD <- bruker.get_param(ACQ,"TD")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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49 SW <- bruker.get_param(ACQ,"SW")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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50 SWH <- bruker.get_param(ACQ,"SW_h")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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51 DTYPA <- bruker.get_param(ACQ,"DTYPA")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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52 BYTORDA <- bruker.get_param(ACQ,"BYTORDA")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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53 #ENDIAN = ifelse( BYTORDA==0, "little", "big")
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54 ENDIAN <- "little"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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55 SIZE = ifelse( DTYPA==0, 4, 8)
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56
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57 PROC <- readLines(PROCFILE)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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58 OFFSET <- bruker.get_param(PROC,"OFFSET")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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59 SI <- bruker.get_param(PROC,"SI")
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60
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61 to.read = file(SPECFILE,"rb")
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62 maxTDSI = max(TD,SI)
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63 # signal<-rev(readBin(to.read, what="int",size=SIZE, n=TD, signed = TRUE, endian = ENDIAN))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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64 signal<-rev(readBin(to.read, what="int",size=SIZE, n=maxTDSI, signed = TRUE, endian = ENDIAN))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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65 close(to.read)
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66
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67 td <- length(signal)
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68
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69 # dppm <- SW/(TD-1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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70 dppm <- SW/(td-1)
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71 pmax <- OFFSET
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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72 pmin <- OFFSET - SW
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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73 ppmseq <- seq(from=pmin, to=pmax, by=dppm)
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74 signal <- 100*signal/max(signal)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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75
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76 SampleSpectrum <- cbind(ppmseq,signal)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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77 return(SampleSpectrum)
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78 }
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79
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80 ## SPECTRUM BUCKETING
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81 NmrBrucker_bucket <- function(spectrum)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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82 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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83 # Initialisations
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84 b <- 1
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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85 j <- 1
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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86 # Variable number
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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87 J <- round((spectrum[1,1]-spectrum[dim(spectrum)[1],1])/bucketSize)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
88 f.bucket <- matrix(rep(0,J*2),ncol=2)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
89 colnames(f.bucket) <- c("Bucket",FileNames[i])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
90
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
91
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
92 # Data bucketing
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
93 while (j < dim(spectrum)[1])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
94 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
95 # chemical shift
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
96 BUB <- spectrum[j,1]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
97
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
98 # In zone exclusion?
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
99 exclusion.in <- FALSE
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
100 if (!is.null(exclusionZonesBorders))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
101 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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102 for (k in 1:nrow(exclusion.zone.m))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
103 if (BUB <= exclusion.zone.m[k,1] && exclusion.zone.m[k,2] < BUB)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
104 exclusion.in <- TRUE
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
105 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
106
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
107 if (exclusion.in)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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108 j <- j + 1
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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109
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
110 if (!exclusion.in)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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111 # Bucketing
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
112 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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113 BLB <- BUB - bucketSize
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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114 bucket <- spectrum[j,]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
115 while (j < dim(spectrum)[1] && spectrum[j,1] > BLB)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
116 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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117 j <- j + 1
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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118 if (spectrum[j,1] > BLB)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
119 bucket <- rbind(bucket,spectrum[j,])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
120 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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121
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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122 # Integration (trapezoid method)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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123 s <- cumtrapz(bucket[,1],bucket[,2])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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124 f.bucket[b,] <- c(round(mean(bucket[,1]),3),abs(s[length(s)][[1]]))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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125
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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126 # Next bucket boundary
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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127 BUB <- spectrum[j,1]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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128 b <- b + 1
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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129 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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130 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
131 return(f.bucket)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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132 }
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133
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marie-tremblay-metatoul
parents:
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134
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marie-tremblay-metatoul
parents:
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135 # File names
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
136 FileNames <- list.files(directory)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
137 n <- length(FileNames)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
138
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
139 # Exclusion zones
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
140 ## if (exclusionZones == "yes")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
141 if (!is.null(exclusionZonesBorders))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
142 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
143 exclusion.zone.m <- matrix(exclusionZonesBorders[[1]],nrow=1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
144 if (length(exclusionZonesBorders) > 1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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145 for (k in 2:length(exclusionZonesBorders))
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
146 exclusion.zone.m <- rbind(exclusion.zone.m,exclusionZonesBorders[[k]])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
147 }
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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148
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marie-tremblay-metatoul
parents:
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149 # Reading and Bucketing
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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150 directory <- paste(directory,"/",sep="")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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151
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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152 i <- 1
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
153 while (i <= n)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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154 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
155 # File reading
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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156 SampleDir <- paste(directory,FileNames[i],"/1/",sep="")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
157 setwd(SampleDir)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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158 DataDir <- "pdata/1"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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159
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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160 rawSpectrum <- NmRBrucker_read(DataDir,rawSpectrum)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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161
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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162 orderedSpectrum <- rawSpectrum[order(rawSpectrum[,1],decreasing=T), ]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
163
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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164 # Removal of chemical shifts > leftBorder or < rightBorder boundaries
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
165 truncatedSpectrum <- orderedSpectrum[orderedSpectrum[,1] < leftBorder & orderedSpectrum[,1] > rightBorder, ]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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166 truncatedSpectrum[,1] <- round(truncatedSpectrum[,1],3)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
167
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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168 # Bucketing
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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169 spectrum.bucket <- NmrBrucker_bucket(truncatedSpectrum)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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170
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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171 # spectrum Concatenation
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
172 if (i == 1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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173 bucketedSpectra <- spectrum.bucket
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
diff changeset
174 if (i > 1)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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175 bucketedSpectra <- cbind(bucketedSpectra,spectrum.bucket[,2])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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176 colnames(bucketedSpectra)[i+1] <- FileNames[i]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
parents:
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177
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178 # Next sample
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179 rm(spectrum.bucket)
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180 i <- i +1
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181 }
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182 identifiants <- gsub("([- , * { } | \\[ ])","_",colnames(bucketedSpectra)[-1])
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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183 colnames(bucketedSpectra) <- c(colnames(bucketedSpectra)[1],identifiants)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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184
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185 bucketedSpectra <- bucketedSpectra[bucketedSpectra[,1]!=0,]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
marie-tremblay-metatoul
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186 rownames(bucketedSpectra) <- paste("B",bucketedSpectra[,1],sep="")
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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187 bucketedSpectra <- bucketedSpectra[,-1]
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188
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189 # Metadata matrice outputs
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190 sampleMetadata <- data.frame(1:n)
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191 rownames(sampleMetadata) <- colnames(bucketedSpectra)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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192 colnames(sampleMetadata) <- "SampleOrder"
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193
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194 variableMetadata <- data.frame(1:nrow(bucketedSpectra))
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195 rownames(variableMetadata) <- rownames(bucketedSpectra)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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196 colnames(variableMetadata) <- "VariableOrder"
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197
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198 # Directory
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199 cd(directory)
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200
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201 # Bucketed spectra graph
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202 if (graph != "None")
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203 {
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204 # Graphic Device opening
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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205 pdf(nomFichier,onefile=TRUE)
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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206
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207 if (graph == "Overlay")
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208 {
3
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lecorguille
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209 x <- 1:length(bucketedSpectra[,1])
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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210 ymax <- max(bucketedSpectra)
3
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lecorguille
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211 plot(x,bucketedSpectra[,1],ylim=c(0,ymax),type='l',col=1,xlab="",xaxt="n",ylab="Intensity")
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lecorguille
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212 # x-axis labels
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213 axis(1, at=seq(1,length(x),by=50),labels=gsub("B","",rownames(bucketedSpectra)[seq(1,length(x),by=50)]), las=2)
0
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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214 for (i in 2:ncol(bucketedSpectra))
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215 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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216 spectre <- bucketedSpectra[,i]
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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217 lines(spectre,col=i)
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218 }
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219 # legend(0,ymax,lty=c(1,1),legend=colnames(bucketedSpectra),col=1:ncol(bucketedSpectra))
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220 }
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221 else
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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222 {
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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223 for (i in 1:ncol(bucketedSpectra))
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224 {
3
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lecorguille
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225 x <- 1:length(bucketedSpectra[,1])
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lecorguille
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226 plot(x,bucketedSpectra[,i],type='l',col=1,xlab="",xaxt="n",ylab="Intensity")
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lecorguille
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227 axis(1, at=seq(1,length(x),by=50),labels=gsub("B","",rownames(bucketedSpectra)[seq(1,length(x),by=50)]), las=2)
0
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228 }
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229 }
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230 dev.off()
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231 }
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232 return(list(bucketedSpectra,sampleMetadata,variableMetadata)) # ,truncatedSpectrum_matrice
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233 }
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234
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235
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236 #################################################################################################################
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237 ## Typical function call
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238 #################################################################################################################
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239 ## StudyDir <- "K:/PROJETS/Metabohub/Bruker/Tlse_BPASourisCerveau/"
a99a6026c972 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
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240 ## upper <- 9.5
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241 ## lower <- 0.8
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242 ## bucket.width <- 0.01
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243 ## exclusion <- TRUE
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244 ## exclusion.zone <- list(c(5.1,4.5))
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245 ## graphique <- "Overlay"
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246 ## nomFichier <- "Tlse_BPASourisCerveau_NmrBucketing_graph.pdf"
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247 ## tlse_cerveaupnd21.bucket <- NmrBucketing(StudyDir,upper,lower,bucket.width,exclusion,exclusion.zone,graphique,nomFichier)
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248 ## write.table(tlse_cerveaupnd21.bucket,file=paste(StudyDir,"Tlse_BPASourisCerveau_NmrBucketing_dataMatrix.tsv",sep=""),
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249 ## quote=FALSE,row.nmaes=FALSE,sep="\t")
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250 #################################################################################################################