R/makeFinalOutput.R

In ELELAB/lipidQ: Lipidomics Analysis Tool

#' @title Make Final Output
#' @author André Vidas Olsen
#' @description This function creates the final output file of the results which
#' consists of both all filtered pmol species and filtered pmol classes.
#' @param classPmol_molPctClass compact output file created by using the
#' compactOutput_pmolCalc() script.
#' @param pmolCalculatedDataSet data of pmol calculations made by using the
#' pmolCalc() script.
#' @param userSpecifiedColnames the column names template file containing user
#' specified column names for the input data.
#' @return a final output file containing pmol and mol% of species
#' @export
#' @examples
#' # load endo & ISTD databases as well as user specified column names file.
#' endogene_lipid_db <- read.table(system.file("extdata/dataTables/checks",
#'  "endogene_lipid_db.csv", package = "lipidQ"), stringsAsFactors = FALSE,
#'  header = TRUE, sep = ",")
#'
#' ISTD_lipid_db <- read.table(system.file("extdata/dataTables/checks",
#'  "ISTD_lipid_db.csv", package = "lipidQ"), stringsAsFactors = FALSE,
#'  header = TRUE, sep = ",")
#'
#' userSpecifiedColnames <- read.table(system.file("extdata/LipidQ_DataBase",
#'  "userSpecifiedColnames.csv", package = "lipidQ"),
#'  stringsAsFactors = FALSE, header = TRUE, sep = ",")
#'
#' # load pmolCalculatedDataSet.csv made by using the pmolCalc() function
#' pmolCalculatedDataSet <- read.table(system.file("extdata/dataTables/checks",
#'  "pmolCalculatedDataSet.csv", package = "lipidQ"),
#'  stringsAsFactors = FALSE, header = TRUE, sep = ",")
#'
#' # make compact output from pmolCalculatedDataSet
#' classPmol_molPctClass_compact <-
#'  compactOutput_pmolCalc(pmolCalculatedDataSet,
#'  userSpecifiedColnames = userSpecifiedColnames)
#'
#' # make final outout
#' finalOutput <- makeFinalOutput(classPmol_molPctClass_compact,
#'  pmolCalculatedDataSet, userSpecifiedColnames = userSpecifiedColnames)
#'
#' # print mol% final output
#' finalOutput[[1]]
#'
#' # print pmol final output
#' finalOutput[[2]]
makeFinalOutput <- function(classPmol_molPctClass, pmolCalculatedDataSet,
                            userSpecifiedColnames = NULL){

  # get colnames for data
  dataColnames <- checkColnames(userSpecifiedColnames = userSpecifiedColnames)



  #### create finalOutput_molPct file

  # take all lipid species (NAME col) from pmolCalculatedDataSet without using
  # the is-rows
  lipidSpecies <- pmolCalculatedDataSet[,c(1,grep("^FILTERED*",
                                              colnames(pmolCalculatedDataSet)))]

  lipidSpecies <- lipidSpecies[-grep("^is",
                                  lipidSpecies[,dataColnames$SUM_COMPOSITION]),]

  # change colnames: NAME -> mol%, FILTERED* -> Sample_01
  sampleNames <- paste0("Sample_",1:(length(colnames(lipidSpecies))-1))
  colnames(lipidSpecies) <- c("molPct", sampleNames)




  # take NAME from classPmol_molPctClass without using the is-rows
  classes <- classPmol_molPctClass[,c(1,
                      grep("^CLASS_FILTERED*",colnames(classPmol_molPctClass)))]
  classes <- classes[-grep("^is",classes[, dataColnames$SUM_COMPOSITION]),]

  # change colnames: NAME -> mol%, CLASS_FILTERED* -> Sample_01
  sampleNames <- paste0("Sample_",1:(length(colnames(classes))-1))
  colnames(classes) <- c("molPct", sampleNames)




  # merge data sets together
  output_molPct <- rbind(lipidSpecies, classes)


  # change classes/species with "O-": insert [SPACE] before "O-" and remove
  # [SPACE] after "O-"
  namesWithOIndexes <- grep("O-",output_molPct$"molPct")
  for(i in namesWithOIndexes){
    nameWithO <- output_molPct$"molPct"[i]
    nameWithO <- strsplit(nameWithO," ")

    if(length(nameWithO[[1]]) == 2){ # used when name represents a specie
      # (contains number specs.)
      nameWithO <- paste0(gsub("O-", " O-",nameWithO[[1]][1]),nameWithO[[1]][2])
    }else{ # used when name represents a class (without number specs.)
      nameWithO <- paste0(gsub("O-", " O-",nameWithO[[1]][1]))
    }
    output_molPct$"molPct"[i] <- nameWithO
  }


  # remove every row that only contains 0's in the columns
  output_molPct <-
    output_molPct[apply(output_molPct[,-1], 1, FUN = function(x) !all(x == 0)),]



  #### create finalOutput_pmol file

  # take all lipid species (NAME col) from pmolCalculatedDataSet without using
  # the is-rows
  lipidSpecies <- pmolCalculatedDataSet[,c(1,grep("^SUBT_PMOL_SAMPLE*",
                  colnames(pmolCalculatedDataSet)))]
  lipidSpecies <- lipidSpecies[-grep("^is",
                  lipidSpecies[, dataColnames$SUM_COMPOSITION]),]

  # change colnames: NAME -> pmol, SUBT_PMOL_SAMPLE* -> Sample_01
  sampleNames <- paste0("Sample_",1:(length(colnames(lipidSpecies))-1))
  colnames(lipidSpecies) <- c("pmol", sampleNames)


  # take NAME from classPmol_molPctClass without using the is-rows
  classes <- pmolCalculatedDataSet[,c(1,grep("^CLASS_PMOL_SUBT_PMOL*",
             colnames(pmolCalculatedDataSet)))]
  classes <- classes[-grep("^is",classes[, dataColnames$SUM_COMPOSITION]),]

  # change colnames: NAME -> pmol, CLASS_PMOL_SUBT_PMOL* -> Sample_01
  sampleNames <- paste0("Sample_",1:(length(colnames(classes))-1))
  colnames(classes) <- c("pmol", sampleNames)

  # remove numbers in the SUM_COMPOSITION column, so only the class name is used
  # for SUM_COMPOSITION.
  for(i in 1:nrow(classes)){
    classes[i, "pmol"] <- unlist(strsplit(classes[i,"pmol"], " "))[[1]]
  }

  # remove rows containing duplicates of SUM_COMPOSITION
  classes <- classes[!duplicated(classes[,"pmol"]),]


  output_pmol <- rbind(lipidSpecies, classes)



  # change classes/species with "O-": insert [SPACE] before "O-" and remove
  # [SPACE] after "O-"
  namesWithOIndexes <- grep("O-",output_pmol$"pmol")
  for(i in namesWithOIndexes){
    nameWithO <- output_pmol$"pmol"[i]
    nameWithO <- strsplit(nameWithO," ")

    if(length(nameWithO[[1]]) == 2){ # used when name represents a specie
      #(contains number specs.)
      nameWithO <- paste0(gsub("O-", " O-",nameWithO[[1]][1]),nameWithO[[1]][2])
    }else{ # used when name represents a class (without number specs.)
      nameWithO <- paste0(gsub("O-", " O-",nameWithO[[1]][1]))
    }
    output_pmol$"pmol"[i] <- nameWithO
  }



  output <- list(output_molPct, output_pmol)

  return(output)
}