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1 if (require("IWTomics",character.only = TRUE,quietly = FALSE)) {
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2 args=commandArgs(TRUE)
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3
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4 # get args names and values
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5 args_values=strsplit(args,'=')
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6 args_names=unlist(lapply(args_values,function(arg) arg[1]))
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7 names(args_values)=args_names
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8 args_values=lapply(args_values,function(arg) arg[2])
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9 # read filenames
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10 adjustedpvalue=args_values$adjustedpvalue
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11 iwtomicsrespdf=args_values$iwtomicsrespdf
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12 iwtomicssumpdf=args_values$iwtomicssumpdf
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13 iwtomicsrdata=args_values$iwtomicsrdata
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14 iwtomicstests=args_values$iwtomicstests
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15 iwtomicsselectedfeatures=args_values$iwtomicsselectedfeatures
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16 test_subset=paste0('c(',strsplit(args_values$test_subset,'\\|')[[1]],')')
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17 feature_subset=paste0('c(',strsplit(args_values$feature_subset,'\\|')[[1]],')')
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18 # read parameters (from test_subset on)
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19 i_scale_subset=which(args_names=='scale_subset')
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20 for(i in i_scale_subset:length(args)){
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21 eval(parse(text=args[[i]]))
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22 }
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23
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24 # load RData
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25 load(iwtomicsrdata)
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26 # read testids and featureids and check them
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27 unlisted=lapply(seq_along(test_subset),
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28 function(i){
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29 test_subset_i=eval(parse(text=test_subset[i]))
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30 feature_subset_i=eval(parse(text=feature_subset[i]))
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31 test_subset_i=rep(test_subset_i,each=length(feature_subset_i))
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32 feature_subset_i=rep(feature_subset_i,length.out=length(test_subset_i))
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33 scale_subset_i=rep(scale_subset[i],length(test_subset_i))
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34 return(list(test_subset=test_subset_i,feature_subset=feature_subset_i,scale_subset=scale_subset_i))
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35 })
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36 test_subset=unlist(lapply(unlisted,function(l) l$test_subset))
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37 feature_subset=unlist(lapply(unlisted,function(l) l$feature_subset))
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38 scale_subset=unlist(lapply(unlisted,function(l) l$scale_subset))
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39 testids=as.character(read.delim(iwtomicstests,header=FALSE,sep='\t',stringsAsFactors=FALSE))
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40 featureids=as.character(read.delim(iwtomicsselectedfeatures,header=FALSE,sep='\t',stringsAsFactors=FALSE))
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41 id_features_subset=featureids[feature_subset]
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42 if(sum(testids!=paste(testInput(regionsFeatures_test)$id_region1,'vs',testInput(regionsFeatures_test)$id_region2))){
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43 write("Wrong test ids.", stderr())
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44 quit(save="no", status=10)
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45 }
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46 if(sum(featureids!=idFeatures(regionsFeatures_test))){
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47 write("Wrong feature ids.", stderr())
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48 quit(save="no", status=20)
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49 }
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50 # retrieve test and features_subset ids
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51 id_features_subset=featureids[feature_subset]
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52 if(sum(duplicated(paste0(test_subset,id_features_subset)))){
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53 write("Two scale thresholds selected for the same test and feature.", stderr())
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54 quit(save="no", status=30)
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55 }
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56 # If scale_subset=0, do not change the threshold
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57 default=(scale_subset==0)
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58 scale_subset=scale_subset[!default]
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59 test_subset=test_subset[!default]
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60 id_features_subset=id_features_subset[!default]
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61
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62 # get scale threshold
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63 scale_threshold=lapply(regionsFeatures_test@test$result,
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64 function(result) unlist(lapply(result,function(feature) feature$max_scale)))
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65 for(i in seq_along(test_subset)){
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66 if(scale_threshold[[test_subset[i]]][id_features_subset[i]]<scale_subset[i]){
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67 write("Scale threshold too high.", stderr())
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68 quit(save="no", status=40)
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69 }
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70 scale_threshold[[test_subset[i]]][id_features_subset[i]]=scale_subset[i]
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71 }
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72
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73 # create adjustedvalue output
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74 pval=adjusted_pval(regionsFeatures_test,scale_threshold=scale_threshold)
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75 for(test in seq_along(pval)){
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76 for(id_feature in idFeatures(regionsFeatures_test)){
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77 write(paste0('Test: ',testids[test],', on feature ',id_feature),
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78 file=adjustedpvalue,append=TRUE,sep='\t')
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79 pval_i=as.data.frame(t(pval[[test]][[id_feature]]))
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80 row.names(pval_i)=paste('Scale',scale_threshold[[test]][[id_feature]])
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81 write.table(pval_i,file=adjustedpvalue,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
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82 write('',file=adjustedpvalue,append=TRUE,sep='\t')
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83 }
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84 }
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85
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86
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87 # plot test results
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88 pdf(iwtomicsrespdf,width=5,height=7)
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89 if(plottype=='boxplot'){
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90 # fix repeated probs
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91 probs=sort(unique(probs))
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92 }else{
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93 probs=c(0.25,0.5,0.75)
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94 }
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95 plotTest(regionsFeatures_test,alpha=testalpha,type=plottype,probs=probs,average=average,size=size,scale_threshold=scale_threshold,ask=FALSE)
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96 dev.off()
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97
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98 # plot summary results
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99 if(groupby!='none'){
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100 tryCatch({
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101 pdf(iwtomicssumpdf,width=15,height=10)
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102 plotSummary(regionsFeatures_test,alpha=summaryalpha,only_significant=only_significant,groupby=groupby,scale_threshold=scale_threshold,ask=FALSE,append=TRUE)
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103 dev.off()
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104 }, error = function(err) {
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105 if (grepl('selected features with different resolution',err$message)) {
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106 write("Group by 'test' but selected features with different resolution.", stderr())
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107 quit(save="no", status=50) #error: groupby 'test' but selected features with different resolution.
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108 }
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109 write("Summary plot error. Please try again.", stderr())
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110 quit(save="no", status=60) #error
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111 })
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112 }
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113
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114 }else{
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115 write("Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
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116 quit(save="no", status=255)
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117 } |
