comparison testandplot.R @ 74:2bb6b44093ba draft

Uploaded 20170619

73:156b29da2f0b

  # retrieve region1, region2 and features_subset ids and check they are in the RData
  id_region1=regionids[region1]
  id_region2=regionids[region2]
  id_features_subset=featureids[features_subset]
  if(length(setdiff(c(id_region1,id_region2),idRegions(regionsFeatures)))!=0){
    quit(save="no", status=10)
    stop('Wrong region ids')
  }
  if(length(setdiff(id_features_subset,idFeatures(regionsFeatures)))!=0){
    quit(save="no", status=20)
    stop('Wrong feature ids')
  }
  if(sum(duplicated(paste0(id_region1,id_region2)))){
    quit(save="no", status=30)
    stop('Same test repeated multiple times.')
  }
  
  # perform test
  tryCatch({
    # fix repeated probs

        write.table(pval,file=adjustedpvaluematrix,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
        write('',file=adjustedpvaluematrix,append=TRUE,sep='\t')
      }
    }
  }, error = function(err) {
    quit(save="no", status=40) #error testing
    stop(err)
  })
  
  # plot test results
  pdf(iwtomicsrespdf,width=5,height=7)
  if(plottype=='boxplot'){

  # create output
  write.table(as.data.frame(t(paste(id_region1,'vs',id_region2))),file=iwtomicstests,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
  write.table(as.data.frame(t(idFeatures(regionsFeatures_test))),file=iwtomicsselectedfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
  save(regionsFeatures_test,file=iwtomicsrdata)
}else{
  quit(save="no", status=255)
  stop("Missing IWTomics package")
}

74:2bb6b44093ba

  # retrieve region1, region2 and features_subset ids and check they are in the RData
  id_region1=regionids[region1]
  id_region2=regionids[region2]
  id_features_subset=featureids[features_subset]
  if(length(setdiff(c(id_region1,id_region2),idRegions(regionsFeatures)))!=0){
    write("Wrong region ids.", stderr())
    quit(save="no", status=10)
  }
  if(length(setdiff(id_features_subset,idFeatures(regionsFeatures)))!=0){
    write("Wrong feature ids.", stderr())
    quit(save="no", status=20)
  }
  if(sum(duplicated(paste0(id_region1,id_region2)))){
    write("Same test repeated multiple times.", stderr())
    quit(save="no", status=30)
  }
  
  # perform test
  tryCatch({
    # fix repeated probs

        write.table(pval,file=adjustedpvaluematrix,append=TRUE,sep='\t',quote=FALSE,row.names=TRUE,col.names=FALSE)
        write('',file=adjustedpvaluematrix,append=TRUE,sep='\t')
      }
    }
  }, error = function(err) {
    write("Testing error.", stderr())
    quit(save="no", status=40) #error testing
  })
  
  # plot test results
  pdf(iwtomicsrespdf,width=5,height=7)
  if(plottype=='boxplot'){

  # create output
  write.table(as.data.frame(t(paste(id_region1,'vs',id_region2))),file=iwtomicstests,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
  write.table(as.data.frame(t(idFeatures(regionsFeatures_test))),file=iwtomicsselectedfeatures,quote=FALSE,sep='\t',row.names=FALSE,col.names=FALSE)
  save(regionsFeatures_test,file=iwtomicsrdata)
}else{
  write("Missing IWTomics package. Please be sure to have it installed before using this tool.", stderr())
  quit(save="no", status=255)
}