R/purityA-constructor.R

In computational-metabolomics/msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

NULL

# msPurity R package for processing MS/MS data - Copyright (C)
#
# This file is part of msPurity.
#
# msPurity is a free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# msPurity is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with msPurity.  If not, see <https://www.gnu.org/licenses/>.



#' @title Assess the acquired precursor ion purity of MS/MS spectra (constructor)
#'
#' @description
#' ## General
#'
#' Given a vector of LC-MS/MS or DI-MS/MS mzML file paths calculate the precursor ion purity of
#' each MS/MS scan.
#'
#' The precursor ion purity represents the measure of the contribution of a selected precursor
#' peak in an isolation window used for fragmentation and can be used as away of assessing the
#' spectral quality and level of "contamination" of fragmentation spectra.
#'
#' The calculation involves dividing the intensity of the selected precursor peak by the total
#' intensity of the isolation window and is performed before and after the MS/MS scan of
#' interest and interpolated at the recorded time of the MS/MS acquisition.
#'
#' Additionally, isotopic peaks are annotated and omitted from the calculation,
#' low abundance peaks are removed that are thought to have minor contribution to the
#' resulting MS/MS spectra and the isolation efficiency of the mass spectrometer can be
#' used to normalise the intensities used for the calculation.
#'
#' The output is a purityA S4 class object (referred to as pa for convenience throughout
#' the manual). The object contains a slot (pa@@puritydf) where the details of the purity
#' assessments for each MS/MS scan. The purityA object can then be used for further processing
#' including linking the fragmentation spectra to XCMS features, averaging fragmentation,
#' database creation and spectral matching (from the created database).
#'
#'
#' ## Example LC-MS/MS processing workflow
#'
#' The purityA object can be used for further processing including linking the fragmentation spectra to XCMS features, averaging fragmentation, database creation and spectral matching (from the created database).
#' See below for an example workflow:
#'
#'  * Purity assessments
#'    +  (mzML files) -> **purityA** -> (pa)
#'  * XCMS processing
#'    +  (mzML files) -> xcms.findChromPeaks -> (optionally) xcms.adjustRtime -> xcms.groupChromPeaks -> (xcmsObj)
#'    +  --- *Older versions of XCMS* --- (mzML files) -> xcms.xcmsSet -> xcms.group -> xcms.retcor -> xcms.group -> (xcmsObj)
#'  * Fragmentation processing
#'    + (xcmsObj, pa) -> frag4feature -> filterFragSpectra -> averageAllFragSpectra -> createDatabase -> spectralMatching -> (sqlite spectral database)
#'
#' ## Isolation efficiency
#'
#' When the isolation efficiency of an MS instrument is known the peak intensities within an isolation window can be normalised for the precursor purity calculation. The isolation efficiency can be estimated by measuring a single precursor across a sliding window. See figure 3 from the original msPurity paper (Lawson et al 2017). This has been experimentally measured  for a Thermo Fisher Q-Exactive Mass spectrometer using 0.5 Da windows and can be set within msPurity by using msPurity::iwNormQE.5() as the input to the iwNormFunc argument.
#'
#' Other options to model the isolation efficiency the  gaussian isolation window msPurity::iwNormGauss(minOff=-0.5, maxOff = 0.5) or a R-Cosine window msPurity::iwNormRCosine(minOff=-0.5, maxOff=0.5). Where the minOff and maxOff can be altered depending on the isolation window size.
#'
#' A user can also define their own normalisation function. The only requirement of the function is that given a value between the minOff and maxOff a normalisation value between 0-1 is returned.
#'
#' ## Notes regarding instrument specific isolation window offsets used:
#'
#' * The isolation widths offsets will be automatically determined from extracting metadata from the mzML file. However, for some vendors though this is not recorded, in these cases the offsets should be given by the user as an argument (offsets).
#'
#' * In the case of Agilent only the "narrow" isolation is supported. This roughly equates to +/- 0.65 Da (depending on the instrument). If the file is detected as originating from an Agilent instrument the isolation widths will automatically be set as +/- 0.65 Da.
#'
#'
#' @param fileList vector; mzML file paths
#' @param mostIntense boolean; True if the most intense peak is used for calculation. Set to FALSE if the peak closest to mz value detailed in mzML meta data.
#' @param nearest boolean; True if the peak selected is from either the preceding scan or the nearest.
#' @param offsets vector; Override the isolation offsets found in the mzML file e.g. c(0.5, 0.5)
#' @param plotP boolean; If TRUE a plot of the purity is to be saved
#' @param plotdir vector; If plotP is TRUE plots will be saved to this directory
#' @param interpol character; type of interolation to be performed "linear" or "spline" (Spline option is only included for testing purposes,
#'                            linear should be used for all standard cases, isotope removal is also not available for the spline option)
#' @param iwNorm boolean; If TRUE then the intensity of the isolation window will be normalised based on the iwNormFun function
#' @param iwNormFun function; A function to normalise the isolation window intensity. The default function is very generalised and just accounts for edge effects
#' @param ilim numeric; All peaks less than this percentage of the target peak will be removed from the purity calculation, default is 5% (0.05)
#' @param isotopes boolean; TRUE if isotopes are to be removed
#' @param im matrix; Isotope matrix, default removes C13 isotopes (single, double and triple bonds)
#' @param mzRback character; backend to use for mzR parsing
#' @param ppmInterp numeric; Set the ppm tolerance for the precursor ion purity interpolation. i.e. the ppm tolerence between
#'                           the precursor ion found in the neighbouring scans.
#' @param cores numeric; Number of cores to use
#'
#' @return Returns a purityA object (pa) with the pa@@puritydf slot updated
#'
#' The purity dataframe (**pa@@puritydf**) consists of the following columns:
#' * pid: unique id for MS/MS scan
#' * fileid: unique id for mzML file
#' * seqNum: scan number
#' * precursorIntensity: precursor intensity value as defined in the mzML file
#' * precursorMZ: precursor m/z value as defined in the mzML file
#' * precursorRT: precursor RT value as defined in the mzML file
#' * precursorScanNum: precursor scan number value as defined in mzML file
#' * id: unique id (redundant)
#' * filename: mzML filename
#' * precursorNearest: MS1 scan nearest to the MS/MS scan
#' * aMz: The m/z value in the "precursorNearest" MS1 scan which most closely matches the precursorMZ value provided from the mzML file
#' * aPurity: The purity score for aMz
#' * apkNm: The number of peaks in the isolation window for aMz
#' * iMz: The m/z value in the precursorNearest MS1 scan that is the most intense within the isolation window.
#' * iPurity: The purity score for iMz
#' * ipkNm: The number of peaks in the isolation window for iMz
#' * inPurity: The interpolated purity score (the purity score is calculated at neighbouring MS1 scans and interpolated at the point of the MS/MS acquisition)
#' * inpkNm: The interpolated number of peaks in the isolation window
#'
#' The remaining slots for purityA class include
#' * pa@@cores: The number of CPUs to be used for any further processing with this purityA object
#' * pa@@fileList: list of the mzML files that have been processed
#' * pa@@mzRback: The backend library used by mzR to extract information from the mzML file (e.g. pwiz)
#' * pa@@grped_df: If frag4feature has been performed, a dataframe of the grouped XCMS features linked to the associated fragmentation spectra precursor details is recorded here
#' * pa@@grped_ms2:  If frag4feature has been performed, a list of fragmentation spectra associated with each grouped XCMS feature is recorded here
#' * pa@@f4f_link_type: If frag4feature has been performed, the 'linking method' is recorded here, e.g. 'group' or 'individual'. Default is 'individual', see frag4feature documentation for more details
#' * pa@@av_spectra: if averageIntraFragSpectra, averageInterFragSpectra,  or averageAllFragSpectra have been performed, the average spectra is recorded here
#' * pa@@av_intra_params:  If averageIntraFragSpectra has been performed, the parameters are recorded here
#' * pa@@av_inter_params: if averageInterFragSpectra has been performed, the  parameters are recorded here]
#' * pa@@av_all_params: If averageAllFragSpectra has been performed, the parameters are recorded here
#' * pa@@db_path: If create_database has been performed, the resulting path to the database is recorded here
#'
#' @examples
#' filepths <- system.file("extdata", "lcms", "mzML", "LCMSMS_1.mzML", package="msPurityData")
#' pa <- purityA(filepths)
#' @seealso \code{\link{assessPuritySingle}}
#' @md
#' @export
purityA <- function(fileList,
                    cores=1,
                    mostIntense=FALSE,
                    nearest=TRUE,
                    offsets=NA,
                    plotP=FALSE,
                    plotdir=NULL,
                    interpol="linear",
                    iwNorm=FALSE,
                    iwNormFun=NULL,
                    ilim=0.05,
                    mzRback='pwiz',
                    isotopes=TRUE,
                    im=NULL,
                    ppmInterp=7){

  if((is.null(fileList)) || (all(fileList == "" ))){
    message("no file list")
    return(NULL)
  }
  names(fileList) <- basename(fileList)

  requireNamespace('foreach')
  pa <- new("purityA", fileList = fileList, cores = cores, mzRback=mzRback)

  # Check cores and choose if parallel or not (do or dopar)
  if(pa@cores<=1){
    operator <- foreach::'%do%'
  } else{
    cl1 <- parallel::makeCluster(pa@cores, type="SOCK")
    doSNOW::registerDoSNOW(cl1)
    operator <- foreach::'%dopar%'
  }



  # run parallel (or not) using foreach
  purityL <- operator(foreach::foreach(i = 1:length(pa@fileList),
                                  .packages = 'mzR'),
                                  assessPuritySingle(filepth = pa@fileList[[i]],
                                  mostIntense = mostIntense,
                                  nearest=nearest,
                                  offsets = offsets,
                                  plotP = plotP,
                                  plotdir = plotdir,
                                  interpol = interpol,
                                  iwNorm = iwNorm,
                                  iwNormFun = iwNormFun,
                                  ilim = ilim,
                                  mzRback = mzRback,
                                  isotopes = isotopes,
                                  im = im,
                                  ppmInterp = ppmInterp
                                  ))

  if(pa@cores>1){
      parallel::stopCluster(cl1)
  }

  names(purityL) <- seq(1, length(purityL))

  puritydf <- plyr::ldply(purityL, .id = TRUE)

  if(nrow(puritydf)>0){
    colnames(puritydf)[1] <- "fileid"
    pid <- seq(1, nrow(puritydf))
    puritydf <- cbind(pid, puritydf)
  }

  pa@puritydf <- puritydf
  pa@cores = cores

  return(pa)
}


#' @title Assess the purity of a single LC-MS/MS or DI-MS/MS file
#'
#' @description
#'
#' Given a filepath to an mzML file the precursor purity for any MS/MS scans
#' will be outputed into a dataframe
#'
#' @param filepth character; mzML file path for MS/MS spectra
#' @param fileid numeric; adds a fileid column (primarily for internal use for msPurity)
#' @param mostIntense boolean; True if the most intense peak is used for calculation. False if the centered peak is used
#' @param nearest boolean; True if the peak selected is as the nearest MS1 scan. If False then the preceding scan is used
#' @param offsets vector; Overide the isolation offsets found in the mzML filee.g. c(0.5, 0.5)
#' @param cores numeric; Number of cores to use
#' @param plotP boolean; If TRUE a plot of the purity is to be saved
#' @param plotdir vector; If plotP is TRUE plots will be saved to this directory
#' @param interpol character; Type of interolation to be performed "linear", "spline" or "none"
#' @param iwNorm boolean; If TRUE then the intensity of the isolation window will be normalised based on the iwNormFun function
#' @param iwNormFun function; A function to normalise the isolation window intensity. The default function is very generalised and just accounts for edge effects
#' @param ilim numeric; All peaks less than this percentage of the target peak will be removed from the purity calculation, default is 5% (0.05)
#' @param mzRback character; Backend to use for mzR parsing
#' @param isotopes boolean; TRUE if isotopes are to be removed
#' @param im matrix; Isotope matrix, default removes C13 isotopes (single, double and triple bonds)
#' @param ppmInterp numeric; Set the ppm tolerance for the precursor ion purity interpolation. i.e. the ppm tolerence between
#'                           the precursor ion found in the neighbouring scans.
#' @return a dataframe of the purity score of the ms/ms spectra
#'
#' @examples
#' filepth <- system.file("extdata", "lcms", "mzML", "LCMSMS_1.mzML", package="msPurityData")
#'
#' puritydf <- assessPuritySingle(filepth)
#' @seealso \code{\link{purityA}}
#' @export
assessPuritySingle <- function(filepth,
                               fileid=NA,
                               mostIntense=FALSE,
                               nearest=TRUE,
                               offsets=NA,
                               cores=1,
                               plotP=FALSE,
                               plotdir=NULL,
                               interpol="linear",
                               iwNorm=FALSE,
                               iwNormFun=NULL,
                               ilim=0,
                               mzRback='pwiz',
                               isotopes=TRUE,
                               im=NULL,
                               ppmInterp=7){
  #=================================
  # Load in files and initial setup
  #=================================
  # Get the mzR dataframes
  mrdf <- getmrdf(filepth, mzRback)
  if(is.null(mrdf)){
    message(paste("No MS/MS spectra for file: ", filepth))
    return(NULL)
  }

  # having id column makes things easier to track
  mrdf$id <- seq(1, nrow(mrdf))

  # add the fileid info
  if(!is.na(fileid)){
    mrdf$fileid <- rep(fileid, nrow(mrdf))
  }

  # add filename
  mrdf$filename <- basename(filepth)

  # Get a shortened mzR dataframe
  mrdfshrt <- mrdf[mrdf$msLevel==2,][,c("seqNum","acquisitionNum","precursorIntensity",
                                        "precursorMZ", "precursorRT",
                                        "precursorScanNum", "id", "filename", "retentionTime")]

  if((length(unique(mrdf$msLevel))<2) && (unique(mrdf$msLevel)==2)){
    message("only MS2 data, not possible to calculate purity")
    mrdfshrt[ , c("precursorNearest", "aMz", "aPurity", "apkNm", "iMz", "iPurity", "ipkNm", "inPkNm", "inPurity")] <- NA
    return(mrdfshrt)
  }

  # get scans (list of mz and i) from mzR
  scans <- getscans(filepth, mzRback)

  # Get offsets from mzML unless defined by user
  if(anyNA(offsets)){
    offsets <- get_isolation_offsets(filepth)
  }
  minoff <- offsets[1]
  maxoff <- offsets[2]

  if(is.null(iwNormFun)){
    iwNormFun <- iwNormGauss(minOff = -minoff, maxOff = maxoff)
  }




  # For n MS1 scans before and after the MS2 scan. For linear interpolation
  # only two points needed. More needed for spline
  if((interpol=="linear") || (interpol=="none")){
    # if linear interpolation we only need the purity before and after.
    # If no interpolation required we still need to find the nearest ms1 scan
    # so the nump is 1 as well
    nump <- 1
  }else if (interpol=="spline"){
    # if performing spline we need multiple data points
    nump <- 10
  }

  # Get the precursor (ms1) scans
  prec_scans <- get_prec_scans(mrdf, nump)

  # add a column with the nearest precursor for all ms2 scans
  mrdfshrt$precursorNearest <- plyr::laply(prec_scans, function(x){ return(x$nearest)})


  #=====================================
  # Initial purity calculation
  #=====================================
  # Get the initial purity score and target mz associated with every ms2 scan.
  # Calculate the purity on the nearest ms1 scan. This function also determines
  # which is the target peak used for interpolations
  initial <- plyr::ddply(mrdfshrt, ~ seqNum, get_init_purity,
                           scans=scans,
                           minoff=minoff,
                           maxoff=maxoff,
                           nearest=nearest,
                           mostIntense=mostIntense,
                           iwNorm=iwNorm,
                           iwNormFun=iwNormFun,
                           ilim=ilim,
                           isotopes=isotopes,
                           im=im)

  # Add results to mzR dataframe
  mrdfshrt <- cbind(mrdfshrt, initial)

  # If no interpolation required then all purity calculations are completed
  if(interpol=="none"){
    return(mrdfshrt)
  }

  #=====================================
  # Interpolation
  #=====================================
  # The interpolation can be time consuming if using spline interpolation,
  # so can be run in parallel
  if(cores>1){
    requireNamespace(parallel)
    clust<-parallel::makeCluster(cores)
    doSNOW::registerDoSNOW(clust)
    pBool = TRUE
  }else{
    pBool = FALSE
  }

  interDF <- plyr::ddply(mrdfshrt, ~ seqNum, .parallel = pBool,
                                   get_interp_purity, # FUNCTION
                                   scan_peaks=scans,
                                   ppm=ppmInterp,
                                   ms2=mrdf[mrdf$msLevel==2,]$seqNum,
                                   prec_scans=prec_scans,
                                   minoff=minoff,
                                   maxoff=maxoff,
                                   mostIntense=mostIntense,
                                   plotP=plotP,
                                   plotdir=plotdir,
                                   interpol=interpol,
                                   nearest=nearest,
                                   iwNorm=iwNorm,
                                   iwNormFun=iwNormFun,
                                   ilim=ilim,
                                   isotopes=isotopes,
                                   im=im)

  if(cores>1){
    requireNamespace(parallel)
    parallel::stopCluster(clust)
  }

  if(interpol=="spline"){
    mrdfshrt$inPurity <- interDF$inPurity
  }else{
    mrdfshrt$inPkNm <- interDF$inPkNm
    mrdfshrt$inPurity <- interDF$inPurity
  }


  return(mrdfshrt)

}


get_init_purity <- function(ms2h, scans, minoff, maxoff, nearest,
                            mostIntense, iwNorm, iwNormFun, ilim, isotopes, im){

  #========================================
  # Get the scan to perform calculations on
  #========================================
  if (nearest){
    precScn <- ms2h$precursorNearest
  }else{
    precScn <- ms2h$precursorScanNum
  }

  # What the mzML says the mz and intensity of the target is
  precMZ <- ms2h$precursorMZ
  precI <- ms2h$precursorIntensity

  mzmin <-  precMZ - minoff
  mzmax <-  precMZ + maxoff

  allscans <- scans[[precScn]]

  #=======================================
  # Get centered target peak
  #=======================================
  # Get target based on matching to be within isolation window of precursorMZ
  # and 1 decimal of intensity
  target_approx <- allscans[(allscans[,1]>=mzmin) & (allscans[,1]<=mzmax)
                            & (round(allscans[,2],1) == round(precI,1)),]

  # no precusor within isolation window and itensity
  if(length(target_approx)==0){
    # get nearest match for just mz
    target_approx <- allscans[(allscans[,1]>=mzmin) & (allscans[,1]<=mzmax),]
    if(length(target_approx)==0){
      return(c("aMz"= NA, "aPurity" = 0, "apkNm" = NA,
               "iMz" = NA, "iPurity" = 0, "ipkNm" = NA ))
    }
  }

  if (length(target_approx)==2) {
    target <- target_approx
  }else{
    # Get the mz that is closest to the target
    target <- target_approx[which.min(abs(target_approx[,1]- precMZ)),]
  }

  # The centered peak
  aMz <- unname(target[1])

  #==================================================
  # Get most intense peak within isolation window
  #==================================================
  subp <- allscans[(allscans[,1]>=mzmin) & (allscans[,1]<=mzmax),  ]

  if(is.vector(subp)){
    iTarget <- subp
  }else if (nrow(subp)==0){
    # nothing within in the mz tolerance range
    return(c("aMz"=aMz, "aPurity" = 0, "iMz" = NA, "iPurity" = 0 ))
  }else{
    iTarget <- subp[order(subp[,2], decreasing = TRUE),][1,]
  }

  # the most intense peak
  iMz <- unname(iTarget[1])

  #==================================================
  # Calculate initial purity
  #==================================================
  if(is.vector(subp)){
    aPurity = iPurity = apkNm = ipkNm =  1
  } else if (nrow(subp)==1){
    aPurity = iPurity = apkNm = ipkNm =  1

  } else {
    pouta <- pcalc(peaks=subp, mzmin=mzmin, mzmax=mzmax, mztarget=aMz, ppm=NA,
                   iwNorm=iwNorm, iwNormFun=iwNormFun, ilim=ilim, isotopes=isotopes,
                   im=im)
    aPurity <- unname(pouta[1])
    apkNm <- unname(pouta[2])
    pouti <- pcalc(peaks=subp, mzmin=mzmin, mzmax=mzmax, mztarget=iMz, ppm=NA,
                   iwNorm=iwNorm, iwNormFun=iwNormFun, ilim=ilim, isotopes=isotopes,
                   im=im)
    iPurity <- unname(pouti[1])
    ipkNm <- unname(pouti[2])

  }
  fileinfo <- c("aMz"=aMz, "aPurity" = aPurity, "apkNm" = apkNm,
                "iMz" = iMz, "iPurity" = iPurity, "ipkNm" = ipkNm )
  return(fileinfo)

}

get_interp_purity <- function(rowi, scan_peaks, prec_scans, ms2, ppm,
                              minoff, maxoff, mostIntense=FALSE, plotP=FALSE,
                              plotdir=NULL, interpol, nearest=TRUE,
                              iwNorm, iwNormFun, ilim, isotopes, im){

  # get the region of interest for scans
  scanids <- prec_scans[which(ms2==rowi$seqNum)][[1]]
  roi_scns <- scan_peaks[c(scanids$pre, scanids$post)]

  if(interpol=="linear"){
    purity <- linearPurity(rowi, scan_peaks, minoff, maxoff, ppm, scanids,
                           nearest, mostIntense, iwNorm, iwNormFun,
                           ilim, plotP, plotdir, isotopes, im)
  }else if (interpol=="spline"){
    purity <- splinePurity(rowi, roi_scns, minoff, maxoff, ppm,
                           mostIntense, scanids, plotP, plotdir)
  }


  return(purity)

}

linearPurity <- function(rowi, scan_peaks, minoff, maxoff, ppm, scanids,
                         nearest, mostIntense, iwNorm, iwNormFun, ilim,
                         plotP, plotdir, isotopes, im){
  if(nearest){
    scn1 <- rowi$precursorNearest
  }else{
    scn1 <- rowi$precursorScanNum
  }

  if(mostIntense){
    purity1 <- rowi$iPurity
    mztarget1 <- rowi$iMz
    pknm1 <- rowi$ipkNm
  }else{
    purity1 <- rowi$aPurity
    mztarget1 <- rowi$aMz
    pknm1 <- rowi$apkNm
  }

  precMZ <- rowi$precursorMZ

  mzmin <-  precMZ - minoff
  mzmax <-  precMZ + maxoff


  # Calculate ppm tolerance to look either side of the original target value
  targetMaxMZ <- mztarget1 + (mztarget1*0.000001)*ppm
  targetMinMZ <- mztarget1 - (mztarget1*0.000001)*ppm


  # Then calculate purity for the other nearest MS1 scan (purity2)
  if(scanids$pre==scn1){
    scn2 <- scanids$post
  }else{
    scn2 <- scanids$pre
  }

  # The last scan (nothing to interpolate from)
  if((length(scn2)==0) || (is.na(mztarget1))){
    return(c("inPkNm"=pknm1, "inPurity"=purity1))
  }

  # Calculate purity for the other nearest MS1 scan
  allp <- scan_peaks[[scn2]]

  pout <- pcalc(peaks=allp, mzmin=mzmin, mzmax=mzmax, mztarget=mztarget1,
                iwNorm=iwNorm, iwNormFun=iwNormFun, ilim=ilim,
                targetMinMZ = targetMinMZ, targetMaxMZ = targetMaxMZ,
                isotopes = isotopes, im = im)

  purity2 <- pout[1]
  pknm2 <- pout[2]



  ###########################################
  # Interpolate for purity
  ###########################################
  # Cant interpolate if only have 1 NA value
  if(is.na(purity2)){
    inPurity <- purity1
    fpurity <- NULL
  }else if (is.na(purity1)){
    inPurity <- purity2
    fpurity <- NULL
  }else{
    # Create linear functions for poth purity and the number of peaks
    fpurity <- approxfun(c(scn1, scn2), c(purity1, purity2))
    inPurity <- fpurity(scanids$scan)
  }

  ###########################################
  # Interpolate for peak number
  ###########################################
  if(is.na(pknm2)){
    inPkNm <- pknm1
  }else if (is.na(pknm1)){
    inPkNm <- pknm2
  }else{
    # Create linear functions for poth purity and the number of peaks
    fpk <- approxfun(c(scn1, scn2), c(pknm2, pknm2))
    inPkNm <- fpk(scanids$scan)
  }

  # save a plot of the interpolation
  if(plotP){
    df <- data.frame("idx"=c(scn1, scn2),"purity"=c(purity1, purity2))
    intername <- paste(rowi$file, "_", rowi$id, "_interpolate_plot_",
                       mztarget1,".png", sep="")
    name <- file.path(plotdir, intername)
    plotPurity(df, rowi$seqNum, name, fpurity)
  }

  return(c("inPkNm"=inPkNm, "inPurity"=inPurity))
}

get_prec_scans <- function(mrdf, num){

  ms1 <- mrdf[mrdf$msLevel==1,]$seqNum
  ms2 <- mrdf[mrdf$msLevel==2,]$seqNum

  prec_scans <- plyr::alply(ms2, 1, function(scan2){
    post <- ms1[ms1>scan2]
    pre <- ms1[ms1<scan2]

    if(length(pre)>num){
      pre <- pre[(length(pre)-(num-1)):length(pre)]
    }

    if(length(post)>num){
      post <- post[1:num]
    }

    nearest <- ms1[which.min(abs(ms1 - scan2))]

    return(list("pre"=pre, "post"=post, "scan"=scan2, "nearest"= nearest))
  })

  return(prec_scans)

}

get_isolation_offsets <- function(inputfile){

  con  <- file(inputfile, open = "r")
  lowFound = FALSE
  highFound = FALSE

  while (TRUE) {
    oneLine <- readLines(con, n = 1)

    if (!lowFound){
      low <- as.numeric(stringr::str_match(oneLine, '^.*name=\"isolation window lower offset\" value=\"([0-9]+\\.[0-9]+).*$')[,2])
      if(!is.na(low)){lowFound=TRUE}
    }

    if (!highFound){
      high <- as.numeric(stringr::str_match(oneLine, '^.*name=\"isolation window upper offset\" value=\"([0-9]+\\.[0-9]+).*$')[,2])
      if(!is.na(high)){highFound=TRUE}
    }

    if (grepl('<cvParam cvRef="MS" accession="MS:1000490" name="Agilent instrument model" value=""/>', oneLine)){
      message("Agilent do not have isolation offset in mzML, default given as +- 0.65 (this is an approximate for the 'narrow' window type)")
      return(c(0.65, 0.65))
    }

    if(lowFound & highFound){
      break
    }
  }

  close(con)
  return(c(low, high))

}


# Get the Data
getmrdf <- function(files, backend='pwiz'){
  #requireNamespace('mzR') # problem with cpp libraries
  # need to be loaded here for parallel
  mrdf <- NULL

  for(i in 1:length(files)){
    #message(paste("processing file:" ,i))
    mr <- mzR::openMSfile(files[i], backend=backend)
    mrdfn <- mzR::header(mr)
    if(length(unique(mrdfn$msLevel))<2){
      if (unique(mrdfn$msLevel)==1){
        message("only MS1 data")
        next
      }
      #else{
      #  message("only fragmentation data")
      #  next
      #}
    }else{
      if(length(unique(mrdfn$precursorScanNum))<2){
        # Note: will be of length 1 even if no scans associated because
        # the mrdf will be zero for not assigned
        message("MS2 data has no associated scan data, will use most recent full scan for information")
        mrdfn  <- missing_prec_scan(mrdfn)
      }

    }


    #mrdfn$fileid <- rep(i,nrow(mrdfn))
    mrdfn$filename <- rep(basename(files[i]),nrow(mrdfn))
    mrdfn$precursorRT <- NA
    # precursorScanNum matches to the acuisitionNum, get row matching row number and relevant retntion time
    mrdfn[mrdfn$msLevel==2,]$precursorRT <- mrdfn[match(mrdfn[mrdfn$msLevel==2,]$precursorScanNum, mrdfn$acquisitionNum),]$retentionTime

    if(!is.data.frame(mrdf)){
      mrdf <- mrdfn
    }else{
      mrdf <- rbind(mrdf,mrdfn)
    }
  }
  return(mrdf)
}

missing_prec_scan <- function(mrdfn){
  for(i in 1:nrow(mrdfn)){
    if(mrdfn[i,]$msLevel>1){
      # Find most recent ms1 level scan
      for (x in i:1){
        if(mrdfn[x,]$msLevel==1){
          mrdfn[i,]$precursorScanNum = mrdfn[x,]$acquisitionNum
          break
        }
      }
    }
  }
  return(mrdfn)
}

getscans <- function(files, backend='pwiz'){
  if(length(files)==1){
    mr <- mzR::openMSfile(files, backend=backend)
    scan_peaks <- mzR::peaks(mr)
    return(scan_peaks)
  }else{

    scan_peaks <- plyr::alply(files, 1 ,function(x){
      mr <- mzR::openMSfile(x, backend=backend)
      scan_peaks <- mzR::peaks(mr)
      return(scan_peaks)
    })

    return(scan_peaks)
  }
}

# MSMSperMS <- function(filepths){
#   l <- lapply(filepths, MSMSperMSsingle)
#   return(plyr::ldply(l, summary))
# }
#
#
# MSMSperMSsingle <- function(filepth){
#   mr <- mzR::openMSfile(filepth)
#   mrdf <- mzR::header(mr)
#
#   m <- mrdf$msLevel
#
#   # First remove repeating ms1 elements
#   c <- 1
#   idx <- c()
#   for (i in 1:length(m)){
#
#     if(i==length(m)){
#       break
#     }
#     if(m[i]==1 && m[i+1]==1) {
#       idx[c] <- i
#       c = c+1
#     }
#   }
#   if(!is.null(idx)){
#     m <- m[-idx]
#   }
#
#
#   # then count how many ms2 are present at each ms1---ms2ms2...ms2---ms1 interval
#   ms2all <- c()
#   c <- 0
#   cidx <- 1
#   for(i in 1:length(m)){
#
#     if(m[i]==2) {
#       c = c+1
#     }
#
#     if(m[i]==2 && (m[i+1]==1 || is.na(m[i+1]))) {
#       ms2all[cidx] <- c
#       cidx = cidx+1
#       c = 0
#     }
#
#   }
#
#   return(ms2all)
#
# }

plotPurity <- function(df, inter, name, f){

  dfm <- reshape2::melt(df, id.vars = c("purity", "idx"))
  png(filename = name)
  p1 <- ggplot2::ggplot(dfm, ggplot2::aes(x=idx, y=purity)) +
    ggplot2::geom_point(ggplot2::aes(colour=variable),shape=20, colour="red") +
    ggplot2::geom_vline(xintercept = inter, colour="red", linetype = "longdash")+
    ggplot2::theme_bw(base_size = 18)+
    ggplot2::theme(text = ggplot2::element_text(size=23))+
    ggplot2::labs(x="scan" , y="precursor purity score") +
    ggplot2::stat_function(fun=f, colour="blue")+
    ggplot2::ylim(0, 1)+
    ggplot2::scale_color_manual(
            "Legend Title\n",labels = c("EIC feature", "+/- 0.5 Contamination"),
             values = c("red", "black") )
  print(p1)
  dev.off()
  dfm$pick <- inter
  saveRDS(f, paste(name, ".rds", sep=""))
  write.csv(dfm, paste(name, ".csv", sep=""), row.names = FALSE)
}