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1 #####################################################
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2 # Mini tools for Galaxy scripting
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3 # Coded by: M.Petera,
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4 # - -
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5 # R functions to use in R scripts and wrappers
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6 # to make things easier (lightening code, reducing verbose...)
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7 # - -
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8 # V0: script structure + first functions
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9 # V1: addition of functions to handle special characters in identifiers
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10 #####################################################
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11
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12
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13 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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14 # Function to call packages without printing all the verbose
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15 # (only getting the essentials, like warning messages for example)
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16
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17 shyLib <- function(...){
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18 for(i in 1:length(list(...))){
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19 suppressPackageStartupMessages(library(list(...)[[i]],character.only=TRUE))
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20 }
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21 }
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22
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23 #example: shyLib("xcms","pcaMethods")
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24
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25
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26
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27 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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28 # Fonction pour sourcer les scripts R requis
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29 # /!\ ATTENTION : actuellement la fonction n'est pas chargee au lancement du script,
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30 # il faut donc la copier-coller dans le wrapper R pour pouvoir l'utiliser.
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31
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32 if(FALSE){
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33 source_local <- function(...){
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34 argv <- commandArgs(trailingOnly = FALSE)
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35 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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36 for(i in 1:length(list(...))){
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37 source(paste(base_dir, list(...)[[i]], sep="/"))
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38 }
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39 }
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40 }
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41
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42 #example: source_local("filter_script.R","RcheckLibrary.R")
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43
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44
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45
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46 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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47 # Functions to stock identifiers before applying make.names() and
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48 # to reinject it into final matrices
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49 # Note: it reproduces the original order of datasets' identifiers
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50 # - - -
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51 # stockID: stocks original identifiers and original order
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52 # -> needs checked data regarding table match
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53 # reproduceID: reinjects original identifiers and original order into final tables
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54 # -> function to be used at the very end, when exporting tables
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55
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56 stockID <- function(dataMatrix, Metadata, Mtype){
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57 # dataMatrix = data.frame containing dataMatrix
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58 # Metadata = data.frame containing sampleMetadata or variableMetadata
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59 # Mtype = "sample" or "variable" depending on Metadata content
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60 cname <- colnames(dataMatrix)[1]
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61 # dataMatrix temporary-stock + transfo - - - -
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62 if(Mtype=="sample"){
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63 id.ori <- colnames(dataMatrix)[-1]
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64 colnames(dataMatrix) <- make.names(colnames(dataMatrix))
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65 }
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66 if(Mtype=="variable"){
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67 id.ori <- dataMatrix[,1]
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68 dataMatrix[,1] <- make.names(dataMatrix[,1])
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69 }
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70 # global stock - - - - - - - - - - - - - - - -
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71 id.new <- data.frame(order.ori=c(1:length(Metadata[,1])),Metadata[,1],
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72 id.new=make.names(Metadata[,1]),id.ori,
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73 id.new.DM=make.names(id.ori),stringsAsFactors=FALSE)
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74 colnames(id.new)[c(2,4)] <- c(colnames(Metadata)[1],cname)
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75 # Metadata transfo + returning data - - - - -
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76 Metadata[,1] <- make.names(Metadata[,1])
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77 return(list(id.match=id.new, dataMatrix=dataMatrix, Metadata=Metadata))
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78 }
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79 #example: A<-stockID(myDM,mysM,"sample") ; myDM<-A$dataMatrix ; mysM<-A$Metadata ; A<-A$id.match
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80
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81 reproduceID <- function(dataMatrix, Metadata, Mtype, id.match){
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82 # dataMatrix = data.frame containing dataMatrix
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83 # Metadata = data.frame containing sampleMetadata or variableMetadata
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84 # Mtype = "sample" or "variable" depending on Metadata content
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85 # id.match = 'id.match' element produced by stockID
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86 #Metadada - - - - - - - - - - - - - -
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87 temp.table <- id.match[,c(1,2,3)]
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88 ## Removing deleted rows
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89 for(i in 1:(dim(id.match)[1])){
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90 if(!(temp.table[i,3]%in%Metadata[,1])){temp.table[i,1] <- 0}
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91 }
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92 if(length(which(temp.table[,1]==0))!=0){
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93 temp.table <- temp.table[-c(which(temp.table[,1]==0)),]
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94 }
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95 ## Restoring original identifiers and order
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96 temp.table <- merge(x=temp.table,y=Metadata,by.x=3,by.y=1)
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97 temp.table <- temp.table[order(temp.table$order.ori),]
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98 Metadata <- temp.table[,-c(1,2)]
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99 rownames(Metadata) <- NULL
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100 #dataMatrix - - - - - - - - - - - - -
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101 rownames(dataMatrix)<-dataMatrix[,1]
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102 if(Mtype=="sample"){
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103 dataMatrix <- t(dataMatrix[,-1])
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104 }
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105 temp.table <- id.match[,c(1,4,5)]
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106 ## Removing deleted rows
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107 for(i in 1:(dim(id.match)[1])){
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108 if(!(temp.table[i,3]%in%rownames(dataMatrix))){temp.table[i,1] <- 0}
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109 }
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110 if(length(which(temp.table[,1]==0))!=0){
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111 temp.table <- temp.table[-c(which(temp.table[,1]==0)),]
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112 }
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113 ## Restoring original identifiers and order
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114 temp.table <- merge(x=temp.table,y=dataMatrix,by.x=3,by.y=0)
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115 temp.table <- temp.table[order(temp.table$order.ori),]
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116 if(Mtype=="variable"){
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117 dataMatrix <- temp.table[,-c(1,2,4)]
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118 colnames(dataMatrix)[1] <- colnames(id.match)[4]
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119 } else {
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120 rownames(temp.table) <- temp.table[,3]
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121 temp.table <- t(temp.table[,-c(1,2,3)])
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122 dataMatrix <- data.frame(rownames(temp.table),temp.table)
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123 colnames(dataMatrix)[1] <- colnames(id.match)[4]
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124 }
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125 rownames(dataMatrix) <- NULL
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126 # return datasets - - - - - - - - - - -
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127 return(list(dataMatrix=dataMatrix, Metadata=Metadata))
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128 }
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129 #example: B<-reproduceID(myDM,mysM,"sample",A) ; myDM<-B$dataMatrix ; mysM<-B$Metadata
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130
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131
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132
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133 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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