R/exportSetXLSX.R

In kroemerlab/GRMeta: Processing MetX data

exportSetXLSX<-function(obj,outfile,ldata=names(obj$Data),transpose=FALSE,nround=3,characterNA=c("-","NA")){
  
#   .jgc <- function(){
#     ## not sure if this is that utile: http://stackoverflow.com/questions/21937640
#     .jcall("java/lang/System", method = "gc")
#   }   
#   
  if(!inherits(obj, "metaboSet")) stop("This is not a metaboSet object")
  
  ldata=ldata[which(ldata%in%names(obj$Data))]
  
  indf<-function(df,nround,characterNA,what="Var"){
    for(j in names(df)){
      if(is.numeric(df[,j])) df[,j]=round(df[,j],nround)
      df[,j]=as.character(df[,j])
      if(any(is.na(df[,j]))) df[is.na(df[,j]),j]=characterNA 
    }
    df=cbind("Var0000000"=as.character(rownames(df)),df,stringsAsFactors=FALSE)
    names(df)[1]=what
    #   print(names(df))
    df=rbind(names(df),df)
    df
  }
  
  wb <- createWorkbook()  
  cat("Exporting to ",outfile," :\n",sep="")
  toadd=indf(obj$Meta[,which(names(obj$Meta)!="Sid")],nround,characterNA[1],"Sid")
#  .jgc()
  cat("SampleInfos ")
  sheet <- createSheet(wb, sheetName = "SampleInfos")
  addDataFrame(toadd,sheet, col.names=FALSE, row.names=FALSE)
  
  toadd=indf(obj$File[,which(names(obj$File)!="Sid")],nround,characterNA[1],"Sid")
# .jgc()
  cat("FileInfos ")
  sheet <- createSheet(wb, sheetName = "FileInfos")
  addDataFrame(toadd,sheet, col.names=FALSE, row.names=FALSE)
  
  toadd=indf(obj$Annot[,which(names(obj$Annot)!="Analyte")],nround,characterNA[1],"Analyte")
#  .jgc()
  cat("VarInfos ")
  sheet <- createSheet(wb, sheetName = "VarInfos")
  addDataFrame(toadd, sheet, col.names=FALSE, row.names=FALSE)
  
  if(length(ldata)>0){
    for(i in ldata){
      if(transpose) m=round(t(obj$Data[[i]]),nround)
      if(!transpose) m=round(obj$Data[[i]],nround)
      m=apply(m,2,as.character)
      if(transpose) df=cbind("Analyte"=obj$Analyte,m)
      if(!transpose) df=cbind("Sid"=obj$Sid,m)
      df=rbind(colnames(df),df)
      df[is.na(df)]=characterNA[2]
      
      cat(i," ",sep="")
#      .jgc()
      sheet <- createSheet(wb, sheetName = i)
      addDataFrame(df,sheet, col.names=FALSE, row.names=FALSE)
      
    }
  }
  saveWorkbook(wb, outfile) 
}
# 
# exportSetXLSX2<-function(obj,outfile,ldata=names(obj$Data),sortSample=c("sType","InjOrder"),sortAnalyte=c("Method","RT"),transpose=FALSE,nround=3,characterNA=c("-","NA")){
#   
# # ldata=names(obj$Data);sortSample=c("sType","InjOrder");sortAnalyte=c("Method","RT");transpose=FALSE;nround=3;characterNA=c("-","NA")
#   
#   if(!inherits(obj, "metaboSet")) stop("This is not a metaboSet object")
#   
#   ldata=ldata[which(ldata%in%names(obj$Data))]
#   sortAnalyte=sortAnalyte[which(sortAnalyte%in%names(obj$Annot))]
#   sortSample=sortSample[which(sortSample%in%names(obj$Meta))]
#   
#   lsoAna=1:length(obj$Analyte)
#   if(!is.null(sortAnalyte)){
#     lsoAna=paste("order(",paste(paste("obj$Annot$",sortAnalyte,sep=""),collapse=","),")",sep="")
#     lsoAna=eval(parse(text=lsoAna))
#   }
#   
#   lsoSa=1:length(obj$Sid)
#   if(!is.null(sortSample)){
#     lsoSa=paste("order(",paste(paste("obj$Meta$",sortSample,sep=""),collapse=","),")",sep="")
#     lsoSa=eval(parse(text=lsoSa))
#   }
#   
#   indf<-function(df,nround,characterNA,what="Var"){
#     for(j in names(df)){
#       if(is.numeric(df[,j])) df[,j]=round(df[,j],nround)
#       df[,j]=as.character(df[,j])
#       if(any(is.na(df[,j]))) df[is.na(df[,j]),j]=characterNA 
#     }
#     df=cbind("Var0000000"=as.character(rownames(df)),df,stringsAsFactors=FALSE)
#     names(df)[1]=what
#     #   print(names(df))
#     df=rbind(names(df),df)
#     df
#   }
#   
#   cat("Exporting to ",outfile," :\n",sep="")
#   df1=indf(obj$Meta[lsoSa,which(names(obj$Meta)!="Sid")],nround,characterNA[1],"Sid");shn ="SampleInfos"
#   df2=indf(obj$File[lsoSa,which(names(obj$File)!="Sid")],nround,characterNA[1],"Sid");shn=append(shn,"FileInfos")
#   df3=indf(obj$Annot[lsoAna,which(names(obj$Annot)!="Analyte")],nround,characterNA[1],"Analyte");shn=append(shn,"VarInfos")
#   
#   j=3
#   for(i in ldata){
#     j=j+1
#     if(transpose) m=round(t(obj$Data[[i]][lsoSa,lsoAna,drop=FALSE]),nround)
#     if(!transpose) m=round(obj$Data[[i]][lsoSa,lsoAna,drop=FALSE],nround)
#     m=apply(m,2,as.character)
#     #    print(str(m))
#     if(transpose) df=cbind("Analyte"=obj$Analyte[lsoAna],m)
#     if(!transpose) df=cbind("Sid"=obj$Sid[lsoSa],m)
#     #   print(names(df))
#     df=rbind(colnames(df),df)
#     df[is.na(df)]=characterNA[2]
#     eval(expr = parse(text=paste("df",j,"=df",sep="")))
#     shn=append(shn,i)
# #     write.xlsx2(data.frame(df,stringsAsFactors = FALSE),
# #                 file = outfile,col.names=FALSE, row.names=FALSE,append=TRUE,sheetName =i)
#     cat(i," ",sep="")
#   }
#   shn=paste(shn,collapse = ',')
#   ldf=paste(paste("df",1:j,sep=""),collapse=",")
#   eval(expr = parse(text=paste("dataframes2xls:::write.xls(c(",ldf,"), outfile, sh.names =shn,col.names=FALSE,row.names=FALSE)",sep="")))
#   
#   invisible(list(lsoSa,lsoAna))
# }