diff --git a/R/annotSheet.R b/R/annotSheet.R
deleted file mode 100644
index a400764..0000000
--- a/R/annotSheet.R
+++ /dev/null
@@ -1,18 +0,0 @@
-#' annotSheet
-#' @export
-
-
-annotSheet <-
-function(annot_all) {
-  # put accurate m/z into list
-  annot_all$`Accurate m/z` <- lapply(apply(annot_all$`Accurate m/z`,1, function(x){return(list(x))}),function(x){return(matrix(x[[1]],ncol=3))})
-  # Caluclate number of columns in sheet
-  bins <- length(annot_all[[1]])
-  # Build table for each bin
-  annot_info <- list()
-  for (i in 1:bins){
-    annot_info[[i]] <- makeTable(lapply(annot_all,function(x,y){return(x[[y]])},y=i))
-  } 
-  annot_info <- do.call(rbind,annot_info)
-  return(annot_info)
-}
diff --git a/R/annotateFIE.R b/R/annotateFIE.R
deleted file mode 100644
index 11e11af..0000000
--- a/R/annotateFIE.R
+++ /dev/null
@@ -1,29 +0,0 @@
-#' Annotation of FIE-HRMS m/z
-#'
-#' @param explan_mass 
-#' @param data 
-#' @param peaks 
-#' @param mode 
-#' @param ppm 
-#' @param gencors 
-#' @param genmf 
-#' @param genpip 
-#' @param lat 
-#' @export
-
-annotateFIE <-
-function(explan_mass,data,peaks,mode,ppm,gencors=T,genmf=T,genpip=T,lat=list(c(C=0,iC=0,H=0,iH=0,N=0,iN=0,O=0,iO=0,F=0,Na=0,Si=0,P=0,S=0,Cl=0,iCl=0,Br=0,iBr=0,K=0,iK=0),c(C=90,iC=1,H=180,iH=0,N=10,iN=0,O=40,F=0,Na=1,Si=0,P=6,S=5,Cl=0,iCl=0,Br=0,iBr=0,K=1,iK=1,iO=1))){
-  annot_all <- list()
-  annot_all[["Accurate m/z"]] <- cbind(Bin=rownames(explan_mass),explan_mass)
-  if(gencors==T){
-    annot_all[["Correlation Analysis"]] <- corAnalysis(data,rownames(explan_mass),mode=mode)
-  }
-  if(genmf==T){
-    annot_all[["Molecular Formulas"]] <- apply(explan_mass,1,getMF,mode=mode,lat=lat,ppm=ppm)
-    annot_all["Theoretical Isotope Distributions"] <- list(lapply(annot_all$'Molecular Formulas',getIsoDist,mode=mode))
-  }
-  if(genpip==T){
-    annot_all["Putative Ionisation Products"] <- list(lapply(explan_mass[,1],getPIP,mode=mode,ppm=ppm))
-  }
-  return(annot_all)
-}
diff --git a/R/annotateLC.R b/R/annotateLC.R
deleted file mode 100644
index b9a1e9e..0000000
--- a/R/annotateLC.R
+++ /dev/null
@@ -1,17 +0,0 @@
-#' LC annotation
-#' @export
-
-annotateLC <- function(features,data,xset,mode,ppm){
-  peakTab <- peakTable(xset)
-  mz.id <- round(peakTab$mz, digits=2)
-  rt.id <- round(peakTab$rt/60, digits=2)
-  f.id <- paste(mode,"M",mz.id,"T",rt.id,sep="")
-  feat.ind <- which(f.id %in% features)
-  featTab <- data.frame(ID=f.id[feat.ind],peakTab[feat.ind,])
-  cat('\nRunning Correlation Analysis\n')
-  corrAnalysis <- corAnalysisLC(data,features,mode)
-  cat('\nRunning PIP searches\n\n')
-  featPIP <- lapply(featTab$mz,getPIP,mode=mode,ppm=ppm)
-  names(featPIP) <- featTab$ID
-  return(list(featPIP=featPIP,corAnalysis=corrAnalysis,peakTable=data.frame(ID=f.id,peakTab[,1:6])))
-}
diff --git a/R/calcDiff.R b/R/calcDiff.R
index 1e439aa..cb28bdf 100644
--- a/R/calcDiff.R
+++ b/R/calcDiff.R
@@ -2,7 +2,6 @@
 #'
 #' @param mat 
 #' @param mo 
-#' @export
 
 calcDiff <-
 function(mat,mo){
diff --git a/R/corAnalysisLC.R b/R/corAnalysisLC.R
deleted file mode 100644
index cc43774..0000000
--- a/R/corAnalysisLC.R
+++ /dev/null
@@ -1,43 +0,0 @@
-#' corAnalysisLC
-#' @export
-
-corAnalysisLC <- function(data,varlist,mode,pval=0.05){
-  cors <- rcorr(as.matrix(data))
-  cors$P <- apply(cors$P,1,p.adjust,method="bonferroni")
-  cors$r[cors$P>pval] <- 0
-  cors$r[cors$r==1] <- 0
-  cors$r[cors$r < 0] <- 0
-  cors <- cors$r
-  cors <- cors[,colnames(cors) %in% varlist]
-  s <- apply(cors,1,sum)
-  cors <- cors[s>0,]
-  cors.lists <- corLists(cors)
-  cor.names <- sapply(cors.lists,function(x){return(colnames(x)[1])})
-  names(cors.lists) <- cor.names
-  cors.lists <- lapply(cors.lists,function(x){
-    rt <- strsplit(as.character(x[,1]),'T')
-    rt <- as.numeric(sapply(rt,function(x){return(x[2])}))
-    mz <- strsplit(as.character(x[,1]),'T')
-    mz <- sapply(mz,function(x){return(x[1])})
-    mz <- as.numeric(gsub(paste(mode,'M',sep=''),'',mz))
-    return(data.frame(x,mz=mz,rt=rt))
-  })
-  cors.diff <- lapply(names(cors.lists),function(x,l,m){
-    l <- l[[x]]
-    l[,1] <- l$mz
-    l <- l[,1:2]
-    mz <- strsplit(colnames(l)[1],'T')
-    mz <- sapply(mz,function(y){return(y[1])})
-    mz <- gsub('M','',mz)
-    colnames(l)[1] <- mz
-    return(l)
-  },l=cors.lists,m=mode)
-  cors.diff <- lapply(cors.diff,calcDiff,mo=mode)
-  cors.lists <- lapply(1:length(cors.lists),function(x,l,d){
-    l <- l[[x]]
-    d <- d[[x]]
-    return(data.frame(l,d[,3:5]))
-  },l=cors.lists,d <- cors.diff)
-  names(cors.lists) <- cor.names
-  return(cors.lists)
-}
\ No newline at end of file
diff --git a/R/corLists.R b/R/corLists.R
index 4c11190..6b49b4a 100644
--- a/R/corLists.R
+++ b/R/corLists.R
@@ -1,7 +1,6 @@
 #' Aggregate significant correlations into lists for each variable
 #'
 #' @param x 
-#' @export
 
 corLists <-
 function(x) {
diff --git a/R/filterIso.R b/R/filterIso.R
deleted file mode 100644
index 9dad6a0..0000000
--- a/R/filterIso.R
+++ /dev/null
@@ -1,19 +0,0 @@
-#' filterIso
-#' @export
-
-filterIso<-
-function(isos){
-	for (i in 1:length(isos)){
-		curr.iso <- isos[[i]]
-		iso.mat <- matrix(nrow=0,ncol=4)
-		for(x in 1:nrow(curr.iso)){
-			iso <- curr.iso[x,4]
-			iso <- unlist(strsplit(iso," "))
-			if (length(iso) < 3){
-				iso.mat <- rbind(iso.mat,curr.iso[x,])
-			}
-		}
-		isos[[i]] <- iso.mat
-	}
- return(isos)
-}
diff --git a/R/filterMF.R b/R/filterMF.R
deleted file mode 100644
index a1eff0d..0000000
--- a/R/filterMF.R
+++ /dev/null
@@ -1,30 +0,0 @@
-#' Filter generated MFs
-#'
-#' @param MFs 
-#'
-#' @description Filter MFs that have more than one adduct or more than one isotope.
-#' @export
-
-filterMF <-
-function(MFs){
-  mf <- as.character(MFs[,"Clean MF"])
-	mf <- sapply(mf,function(x){y <- strsplit(x,"[.]");return(y)})
-  mf <- lapply(mf,function(x){y <- sapply(x,gsub,pattern="iCl",replacement="ICL");return(y)})
-  mf <- lapply(mf,function(x){y <- sapply(x,gsub,pattern="iO",replacement="Io");return(y)})
-  mf <- lapply(mf,function(x){y <- sapply(x,gsub,pattern="iK",replacement="Ik");return(y)})
-	mf <- unlist(lapply(mf,function(x){y <- !(TRUE %in% (grepl("iC",x) & grepl("Ik",x) || 
-                                                grepl("iC",x) & grepl("Io",x) || 
-                                                grepl("iC",x) & grepl("ICL",x) || 
-                                                grepl("Io",x) & grepl("ICL",x) || 
-                                                grepl("Io",x) & grepl("Ik",x) || 
-                                                grepl("K",x) & grepl("Na",x) || 
-                                                grepl("Na",x) & grepl("Ik",x) || 
-                                                grepl("K",x) & grepl("Cl",x) || 
-                                                grepl("ICL",x) & grepl("K",x) || 
-                                                grepl("K",x) & grepl("Ik",x) || 
-                                                grepl("Cl",x) & grepl("ICL",x)));return(y)}))
-  filtered.mfs <- MFs[which(mf==T),]
-  filtered.mfs <- matrix(filtered.mfs,ncol=6)
-  colnames(filtered.mfs) <- colnames(MFs)
-	return (filtered.mfs)
-}
diff --git a/R/filterPIP.R b/R/filterPIP.R
deleted file mode 100644
index f4b59cf..0000000
--- a/R/filterPIP.R
+++ /dev/null
@@ -1,16 +0,0 @@
-#' filterPIP
-#' @export
-
-filterPIP <- 
-  function(res){
-		patterns <- c("ic acid","keto","<i>","</i>","(R)-","(S)-","-L-","L-","(+)-",
-                  "cis,","cis-","trans-","&beta;-","-D-",
-                  "D-","D.","&gamma;-","-n-","N-","&alpha;-","&alpha;","&beta;")
-		replacements <- c("ate","oxo","","","","","","","","","","","","","","","","","","","","")
-		for(i in 1:length(patterns)){
-			res[,2] <- sapply(res[,2],gsub,pattern=patterns[i],replacement=replacements[i],fixed=TRUE)
-		}
-		res[,2] <- tolower(res[,2])
-		res <- res[!duplicated(res[,2]),]
-		return(res)
-  }
\ No newline at end of file
diff --git a/R/getIsoDist.R b/R/getIsoDist.R
deleted file mode 100644
index e832c71..0000000
--- a/R/getIsoDist.R
+++ /dev/null
@@ -1,23 +0,0 @@
-#' getIsoDist
-#' @export
-
-getIsoDist <- function(mf_res,mode){
-  if(nrow(mf_res)>0){
-    if (mode=="p"){
-	  	charge <- 1
-	  }
-	  if (mode=="n"){
-	  	charge <- -1
-	  }	
-	  iso <- grepl("i",mf_res[,"Clean.MF"],fixed=TRUE)
-	  if(length(which(iso==T))>0){
-		  mf_res <- mf_res[-which(iso==T),]
-	  }
-	  if(nrow(mf_res)>0){
-		  iso_ab <- lapply(as.character(mf_res[,"MF"]),isoDistr,chrg=charge)
-		  iso_ab <- filterIso(iso_ab)
-		  names(iso_ab) <- mf_res[,"MF"]
-		  return(iso_ab)
-	  }
-  }
-}
\ No newline at end of file
diff --git a/R/makeTable.R b/R/makeTable.R
deleted file mode 100644
index e9a8354..0000000
--- a/R/makeTable.R
+++ /dev/null
@@ -1,75 +0,0 @@
-#' makeTable
-#' @export
-
-makeTable <-
-  function(annot_info){
-    # combine iso and mf tables if present
-    MF.iso <- list()
-    if("Molecular Formulas" %in% names(annot_info) & "Theoretical Isotope Distributions" %in% names(annot_info)){
-      if (nrow(annot_info[["Molecular Formulas"]])>0 & !is.null(annot_info[["Theoretical Isotope Distributions"]])){
-        MF.tab <- annot_info[["Molecular Formulas"]]
-        MF.tab <- matrix(apply(MF.tab,2,as.character),ncol=ncol(MF.tab))
-        colnames(MF.tab) <- colnames(annot_info[["Molecular Formulas"]])
-        Iso.tab <- annot_info[["Theoretical Isotope Distributions"]]
-        for (i in 1:nrow(MF.tab)){
-          if(MF.tab[i,3] %in% names(Iso.tab)){
-            iso.cur <- Iso.tab[[which(names(Iso.tab)==MF.tab[i,3])]]
-          } else {
-            iso.cur <- matrix(ncol=4,nrow=1)
-          }
-          colnames(iso.cur) <- c("m.z.1","Prob","rel.Int","Isotope")
-          MF.tab.cur <- matrix(ncol=ncol(MF.tab),nrow=nrow(iso.cur)-1)
-          colnames(MF.tab.cur) <- colnames(MF.tab)
-          MF.tab.cur <- rbind(as.character(MF.tab[i,]),MF.tab.cur)
-          MF.iso.tab <- cbind(MF.tab.cur,iso.cur)
-          MF.iso[[i]] <- MF.iso.tab
-        }
-        MF.iso <- ldply(MF.iso,data.frame,stringsAsFactors=F)
-        MF.iso <- apply(MF.iso,2,as.character)
-        annot_info$`Molecular Formulas` <- MF.iso
-        annot_info <- annot_info[-which(names(annot_info) == "Theoretical Isotope Distributions")]
-      } else {
-        if (nrow(annot_info[["Molecular Formulas"]])>0){
-          MF.iso <- cbind(annot_info[["Molecular Formulas"]],matrix(ncol=4,nrow=nrow(annot_info[["Molecular Formulas"]])))
-        } else {
-          MF.iso <- matrix(ncol=10,nrow=1)
-        }
-          annot_info$`Molecular Formulas` <- MF.iso
-          annot_info <- annot_info[-which(names(annot_info) == "Theoretical Isotope Distributions")]
-      }
-    }
-    # rename columns for each table
-    for (i in names(annot_info)){
-      if (i == "Accurate m/z"){
-        colnames(annot_info[[i]]) <- c("Bin","Accurate Mass","Intensity")
-      }
-      if (i == "Correlation Analysis"){
-        colnames(annot_info[[i]]) <- c("m/z","Coefficient","Difference","Relation_to","Relation_from")
-      }
-      if (i == "Molecular Formulas"){
-        colnames(annot_info[[i]]) <- c( "m/z","Original MF","Clean MF","Theoretical m/z","RDB",
-                                 "PPM Error","m/z","Probability","Relative Intensity","Isotope")
-      }
-      if (i == "Putative Ionisation Product"){
-        colnames(annot_info[[i]]) <- c("m/z","Theoretical m/z","MF","Name","Adduct","PPM Error")
-      }
-    }
-    # calculate number of rows needed for table
-    row <- list()
-    for (i in 1:length(annot_info)){
-        row[[i]] <- dim(annot_info[[i]])[1]
-    }
-    names(row) <- names(annot_info)
-    row <- max(unlist(row))
-    # expand each table to the max row number
-    annot_info <- lapply(annot_info, function(x,row){
-      row.add <- row - nrow(x)
-      new.tab <- matrix(ncol=ncol(x),nrow=row.add)
-      colnames(new.tab) <- colnames(x)
-      new.tab <- rbind(x,new.tab)
-      return(new.tab)
-    },row=row)
-    # combine each table
-    annot_table <- do.call("cbind", annot_info)
-    return(annot_table)
-  }
\ No newline at end of file
diff --git a/R/viewAnnotation.R b/R/viewAnnotation.R
deleted file mode 100644
index 487757d..0000000
--- a/R/viewAnnotation.R
+++ /dev/null
@@ -1,197 +0,0 @@
-#' View annotation output
-#' @name viewAnnotation
-#' @description A shiny app to view the RData output of the annotateFIE function
-#' @author Jasen Finch
-#' @export
-#' 
-viewAnnotation <- function(){
-  options(shiny.maxRequestSize = 20*1024^2)
-  options(digits=10)
-  shinyApp(
-    ui = fluidPage(
-      titlePanel("viewAnnotation"),
-      sidebarLayout(
-        sidebarPanel(
-          fileInput('file1', 'Upload Annotation:',
-                    accept = c(
-                      '.RData'
-                    )
-          ),
-          tags$hr(),
-          radioButtons('mode', 'Mode',
-                       c(Positive='Positive_Mode',
-                         Negative='Negative_Mode')),
-          uiOutput("mz"),
-          tags$hr(),
-          textInput("boxplots","Box Plot Folder Path:"),
-          textInput("binplots","Bin Plot Folder Path:")
-        ),
-        mainPanel( 
-          tabsetPanel(
-            tabPanel("Accurate m/z", dataTableOutput('accurate')),
-            tabPanel("Box Plots", imageOutput('boxplot')),
-            tabPanel("Bin Plots", imageOutput('binplot')),
-            tabPanel("Correlation Analysis", dataTableOutput('correlation')),
-            tabPanel("Molecular Formulas",dataTableOutput('MF')),
-            tabPanel("Theoretical Isotope Distributions",
-                     fluidRow(uiOutput("selectMF")),
-                     fluidRow(tableOutput('IsoDist')),
-                     fluidRow(plotOutput('isoplot'))
-            ),
-            tabPanel("Putative Ionisation Products",
-                     fluidRow(dataTableOutput('PIP'))
-            ),
-            tabPanel("PIP Structures",
-                      fluidRow(uiOutput("selectPIP")),
-                      plotOutput('smile')
-            )
-          )
-        )
-      )
-    ),
-    
-    server = function(input, output) {
-      loadData <- reactive({
-        if(is.null(input$file1)) return(NULL)
-        load(input$file1$datapath)
-        annot.res
-      })
-      availmz <- reactive({
-        if(is.null(loadData())) return(NULL)
-        annot.res <- loadData()
-        annot.res[[input$mode]][["Accurate m/z"]][,1]
-      })
-      availMF <- reactive({
-        if(is.null(loadData())) return(NULL)
-        annot.res <- loadData()
-        names(annot.res[[input$mode]][["Theoretical Isotope Distributions"]][[input$selectedmz]])
-      })
-      availPIP <- reactive({
-        if(is.null(loadData())) return(NULL)
-        annot.res <- loadData()
-        annot.res <- annot.res[[input$mode]][["Putative Ionisation Products"]][[input$selectedmz]][,2]
-        annot.res <- gsub('"','',annot.res)
-        annot.res
-      })
-      output$mz <- renderUI({
-        selectInput('selectedmz', 'm/z', availmz())
-      })
-      output$selectMF <- renderUI({
-        selectInput('selectedMF', 'MF', availMF())
-      })
-      output$selectPIP <- renderUI({
-        selectInput('selectedPIP', 'Putative Ionisation Product', availPIP())
-      })
-      output$accurate <- renderDataTable({
-        if (is.null(loadData())){
-          return(NULL)
-        } else {
-          annot.res <- loadData()
-          res <- annot.res[[input$mode]][["Accurate m/z"]]
-          rownames(res) <- NULL
-          res <- data.frame(res)
-          res[,2:3] <- apply(res[,2:3],2,as.numeric)
-          return(res)
-        }
-      })
-      output$boxplot <- renderImage({
-          files <- list.files(input$boxplots)
-          file <- grep(input$selectedmz,files)
-          if(length(file)>0){
-            path <- paste(input$boxplots,files[file],sep="/")
-          } else {
-            path <- ""
-          }
-          list(src=path)
-      },deleteFile = FALSE)
-      output$binplot <- renderImage({
-        files <- list.files(input$binplots)
-        file <- grep(input$selectedmz,files)
-        if(length(file)>0){
-          path <- paste(input$binplots,files[file],sep="/")
-        } else {
-          path <- ""
-        }
-        list(src=path)
-      },deleteFile = FALSE)
-      output$correlation <- renderDataTable({
-        if (is.null(loadData())){
-          return(NULL)
-        } else {
-          annot.res <- loadData()
-          res <- annot.res[[input$mode]][["Correlation Analysis"]][[input$selectedmz]]
-          names(res)[c(1,4,5)] <- c("Bin","Relation To","Relation From")
-          if(nrow(res)>0){
-            res[,4:5] <- apply(res[,4:5],2,function(x){x[which(x=="NA")] <- "";return(x)})
-            res[,2] <- signif(res[,2],3)
-          }
-          return(res)
-        }
-      })
-      output$MF <- renderDataTable({
-        if (is.null(loadData())){
-          return(NULL)
-        } else {
-          annot.res <- loadData()
-          res <- annot.res[[input$mode]][["Molecular Formulas"]][[input$selectedmz]]
-          names(res)[c(1,2,5,6)] <- c("Measured m/z", "Clean MF", "m/z", "PPM Error")
-          res[,5] <- round(as.numeric(res[,5]),5)
-          res[,6] <- round(as.numeric(res[,6]),3)
-          return(res)
-        }
-      })
-      output$IsoDist <- renderTable({
-        if (is.null(loadData())){
-          return(NULL)
-        } else {
-          annot.res <- loadData()
-          res <- annot.res[[input$mode]][["Theoretical Isotope Distributions"]][[input$selectedmz]][[input$selectedMF]]
-          if(!is.null(res)){
-            colnames(res)[3] <- "Relative Intensity"
-          }
-          return(res)
-        }
-      })
-      output$isoplot <- renderPlot({
-        if (is.null(loadData())){
-          return(NULL)
-        } else {
-          annot.res <- loadData()
-          res <- annot.res[[input$mode]][["Theoretical Isotope Distributions"]][[input$selectedmz]][[input$selectedMF]]
-          if(!is.null(res)){
-            plot(res[,1],res[,3],type="h",col="Blue",xlab="m/z",ylab="Relative Intensity")
-          }
-        }
-      })
-      output$PIP <- renderDataTable({
-        if (is.null(loadData())){
-          return(NULL)
-        } else {
-          annot.res <- loadData()
-          res <- annot.res[[input$mode]][["Putative Ionisation Products"]][[input$selectedmz]]
-          names(res)[c(4,7,8)] <- c("Accurate Mass", "m/z","PPM Error")
-          res[,4] <- round(res[,4],5)
-          res[,7] <- round(res[,7],5)
-          res[,8] <- round(res[,8],3)
-          return(res)
-        }
-      })
-      output$smile <- renderPlot({
-        if (is.null(loadData())){
-          return(NULL)
-        } else {
-        annot.res <- loadData()
-        res <- annot.res[[input$mode]][["Putative Ionisation Products"]][[input$selectedmz]]
-        if(nrow(res)>0){
-          res[,2] <- gsub('"','',res[,2])
-          smile <- res[which(res[,2]==input$selectedPIP),5]
-          par(mar=c(0,0,0,0))
-          sm <- parse.smiles(smile)[[1]]
-          temp1 <- view.image.2d(sm,500,500)
-          plot(NA,NA,xlim=c(1,100),ylim=c(1,100),xaxt='n',yaxt='n',xlab='',ylab='') 
-          rasterImage(temp1,1,1,100,100) # boundaries of raster: xmin, ymin, xmax, ymax. here i set them equal to plot boundaries
-        }
-      }},width=400,height=400)
-    }
-  )
-}
\ No newline at end of file
diff --git a/R/viewAnnotationLC.R b/R/viewAnnotationLC.R
deleted file mode 100644
index c8e1aba..0000000
--- a/R/viewAnnotationLC.R
+++ /dev/null
@@ -1,131 +0,0 @@
-#' viewAnnotationLC
-#' @export
-
-viewAnnotationLC <- function(){
-  options(shiny.maxRequestSize = 20*1024^2)
-  options(digits=10)
-  shinyApp(
-    ui = fluidPage(
-      titlePanel("viewAnnotationLC"),
-      sidebarLayout(
-        sidebarPanel(
-          fileInput('file1', 'Upload Annotation:',
-                    accept = c(
-                      '.RData'
-                    )
-          ),
-          tags$hr(),
-          uiOutput("mz"),
-          tags$hr(),
-          textInput("boxplots","Box Plot Folder Path:")
-        ),
-        mainPanel( 
-          tabsetPanel(
-            tabPanel("Peak Table", dataTableOutput('peakTab')),
-            tabPanel("Box Plots", imageOutput('boxplot')),
-            tabPanel('Correlation Analysis',dataTableOutput('corAnalysis')),
-            tabPanel("Putative Ionisation Products",
-                     fluidRow(dataTableOutput('PIP'))
-            ),
-            tabPanel("PIP Structures",
-                     fluidRow(uiOutput("selectPIP")),
-                     plotOutput('smile')
-            )
-          )
-        )
-      )
-    ),
-    
-    server = function(input, output) {
-      loadData <- reactive({
-        if(is.null(input$file1)) return(NULL)
-        load(input$file1$datapath)
-        featAnnot
-      })
-      availmz <- reactive({
-        if(is.null(loadData())) return(NULL)
-        featAnnot <- loadData()
-        names(featAnnot$featPIP)
-      })
-      availPIP <- reactive({
-        if(is.null(loadData())) return(NULL)
-        featAnnot <- loadData()
-        featAnnot <- featAnnot$featPIP[[input$selectedmz]][,2]
-        featAnnot <- gsub('"','',featAnnot)
-        featAnnot
-      })
-      output$mz <- renderUI({
-        selectInput('selectedmz', 'm/z', availmz())
-      })
-      output$selectPIP <- renderUI({
-        selectInput('selectedPIP', 'Putative Ionisation Product', availPIP())
-      })
-      output$peakTab <- renderDataTable({
-        if (is.null(loadData())){
-          return(NULL)
-        } else {
-          featAnnot <- loadData()
-          res <- featAnnot[["peakTable"]]
-          rownames(res) <- NULL
-          res <- data.frame(res)
-          res[,c('rt','rtmin','rtmax')] <- round(res[,c('rt','rtmin','rtmax')]/60,3)
-          return(res)
-        }
-      })
-      output$boxplot <- renderImage({
-        files <- list.files(input$boxplots)
-        file <- grep(input$selectedmz,files)
-        if(length(file)>0){
-          path <- paste(input$boxplots,files[file],sep="/")
-        } else {
-          path <- ""
-        }
-        list(src=path)
-      },deleteFile = FALSE)
-      output$corAnalysis <- renderDataTable({
-        if (is.null(loadData())){
-          return(NULL)
-        } else {
-          featAnnot <- loadData()
-          res <- featAnnot$corAnalysis[[input$selectedmz]]
-          colnames(res)[1] <- 'ID'
-          colnames(res)[6:7] <- c('Relation To','Relation From')
-          res$r <- round(res$r,3)
-          if(nrow(res)>0){
-            res[,6:7] <- apply(res[,6:7],2,function(x){x[which(x=="NA")] <- "";return(x)})
-          }
-          return(res)
-        }
-      })
-      output$PIP <- renderDataTable({
-        if (is.null(loadData())){
-          return(NULL)
-        } else {
-          featAnnot <- loadData()
-          res <- featAnnot$featPIP[[input$selectedmz]]
-          names(res)[c(4,7,8)] <- c("Accurate Mass", "m/z","PPM Error")
-          res[,4] <- round(res[,4],5)
-          res[,7] <- round(res[,7],5)
-          res[,8] <- round(res[,8],3)
-          return(res)
-        }
-      })
-      output$smile <- renderPlot({
-        if (is.null(loadData())){
-          return(NULL)
-        } else {
-          featAnnot <- loadData()
-          res <- featAnnot$featPIP[[input$selectedmz]]
-          if(nrow(res)>0){
-            res[,2] <- gsub('"','',res[,2])
-            smile <- res[which(res[,2]==input$selectedPIP),5]
-            par(mar=c(0,0,0,0))
-            sm <- parse.smiles(smile)[[1]]
-            temp1 <- view.image.2d(sm,500,500)
-            plot(NA,NA,xlim=c(1,100),ylim=c(1,100),xaxt='n',yaxt='n',xlab='',ylab='') 
-            rasterImage(temp1,1,1,100,100) # boundaries of raster: xmin, ymin, xmax, ymax. here i set them equal to plot boundaries
-          }
-        }},width=400,height=400)
-    }
-  )
-}
\ No newline at end of file