R/table.R

In sebkopf/idp: Process compound specific D/H isotope data collected with isodat

IDP.getEmptyPeakTable<-function(idp) {
  options(stringsAsFactors = FALSE)
  indices <- which(tag(idp$gui$win, "settings")$peakTableColumns$Show)
  df<-do.call("data.frame", lapply(tag(idp$gui$win, "settings")$peakTableColumns$Type[indices], FUN = function(x) do.call(x, list())))
  names(df)<-paste(tag(idp$gui$win, "settings")$peakTableColumns$Column[indices], tag(idp$gui$win, "settings")$peakTableColumns$Units[indices], sep="\n")
  return(df)
}

IDP.getDataPeakTable<-function(idp, peakTable) {
  indices <- which(IDP.getSettings(idp, "peakTableColumns")$Show)
  return(peakTable[,indices])
}

IDP.loadPeakTable<-function(idp, peakTable) {
  if (!is.null(peakTable)) { # peak table available
    tag(idp$gui$win, "dataTable")[] <- IDP.getDataPeakTable(idp, peakTable)
  } else { # no peak table --> just show empty one
    tag(idp$gui$win, "dataTable")[] <- IDP.getEmptyPeakTable(idp)
  }
}

# copy peak table to clipboard
IDP.copyPeakTable<-function(idp) {
  # FIXME: throw warning if there have been changes to the standards that have not be recalculated yet
  cp.copyDF(tag(idp$gui$win, "dataTable")[])
}

# recalculate isotopic value of peak table
IDP.recalculatePeakTable<-function(idp) {
  peakTable <- pn.getAllInfo(idp$gui$pn)$peakTable
  peakTable <- IDP.reevaluatePeaks(peakTable, -151.9, # FIXME this should not be hardcoded!!
                                   mode = IDP.getSettings(idp, "stdsCalc"))
  pn.storeInfo(idp$gui$pn, list(peakTable=peakTable))
  IDP.loadPeakTable(idp, peakTable)
  
  # replot data if tab is open
  if (svalue(idp$gui$fileInfo.nb) == 3) # data tab selected
    IDP.plotData(idp, peakTable) 
  
  IDP.showInfo(idp, paste0(IDP.getSettings(idp, "stdsCalc"), ": Peaks re-evaluated using standards for ", IDP.getSettings(idp, "stdsCalc")), 
               timer=3, okButton=FALSE)
}

# revert to original peak table
IDP.revertPeakTable<-function(idp) {
  if (!is.null(oriPeakTable <- pn.getAllInfo(idp$gui$pn)$originalPeakTable)) {
    if (gconfirm("Do you really want to discard all changes you have made to peak/standard assignments in this file?")) {
      pn.storeInfo(idp$gui$pn, list(peakTable=oriPeakTable))
      IDP.loadPeakTable(idp, oriPeakTable)
    }
  }
}