Nothing
R/FUNFINAL.R
In mqqc: Quality control of LCMS derived proteomic data
Defines functions
FUNFINAL
FUNFINAL <-
function(finalMQQC = "D:/resultsmqqc",folder,sucFolder="_RmqqcFile_Processed",Machines = c("Bibo","Kermit","Grobi","Bert","Tiffy"), dayThresh = 5, RESettings = NULL, RESettingsSep = "_",StandardIDs = c("ECstd","BSA"), placeholder = "PLACEHOLDER" ,ordertype = "source",withinlastyear = T,maxReport = 10){
#StandardIDs[1] = ""
# ToDo Table is not rpeorted # html Path is not set
htmlPdfFold <- "files"
dir.create(finalMQQC, showWarnings = F)
dir.create(allPath <- paste(finalMQQC,"all",sep = "/"), showWarnings = F)
dir.create(ECstdPath <- paste(finalMQQC, StandardIDs[2],sep = "/"), showWarnings = F)
dir.create(ECstdPath <- paste(finalMQQC,"files",sep = "/"), showWarnings = F)
dir.create(paste(finalMQQC ,"TimeLines",sep = "/"),showWarnings = F)
if(length(list.files(finalMQQC,pattern = "example.css",recursive = T))== 0){
unzip(list.files(paste(path.package("mqqc"),"data/",sep = "/"),full.name = T,pattern = "html.zip"),exdir = finalMQQC)
}
HotLink = rep("-",length(Machines))
HotLinkCol = rep("#ffffff",length(Machines))
HotLinkPath = rep("-",length(Machines))
collectListPath <- paste(folder,sucFolder,"list_collect.sqlite",sep = "/")
if(file.exists(collectListPath)){
collectList <- dbreadfile(collectListPath)
}
if(length(collectList) > 0){
# collectList <- read.csv(collectListPath, check.names = F,stringsAsFactors = F)
# collectList <- dbreadfile(collectListPath)
collectList <- collectList[!is.na(collectList$Name),]
if(withinlastyear){
yeard <- max(as.numeric(as.character(collectList$System.Time.s)),na.rm = T)-31536000
collectList$System.Time.s[is.na(collectList$System.Time.s)] <- 0
collectList <- collectList[as.numeric(as.character(collectList$System.Time.s)) > yeard,]
}
collectList <- collectList[!is.na(collectList$msms.count),]
collectList <- cbind(1:dim(collectList)[1],collectList)
collectList <- collectList[!duplicated(collectList$Name),]
Names <- collectList$Name
#RE work TODO
if(length(grep(placeholder,RESettings$REpar)) > 0){
StandardIDsRE <- sapply(StandardIDs ,function(x){gsub(placeholder,x,RESettings$REpar)})
# try(StandardIDsRE <- gsub(paste(RESettingsSep,"$",sep = ""),"", StandardIDsRE))
ECstd <- grep(StandardIDsRE[1],collectList$Name,ignore.case = T)
BSA <- grep(StandardIDsRE[2],collectList$Name,ignore.case = T)
}else{
TempNames <- grepRE( gsub(".raw","_raw",collectList$Name),"\\D*_\\d*_[^_]*_[^_]*")
TempNames <- sapply(strsplit(as.character(TempNames),"_"),function(x){x[length(x)]})
ECstd <- 1:dim(collectList)[1]
ECstd <- ECstd[TempNames == StandardIDsRE[1]]
BSA <- 1:dim(collectList)[1]
BSA <- BSA[TempNames == StandardIDsRE[2]]
}
if(all(StandardIDs != "")){
Normal <- setdiff(1:dim(collectList)[1],unique(c(ECstd,BSA)))
AnalysisType <- "both"
InitList <- list(ECstd,Normal, BSA)
itType = 1
itTypeCov <- F
}
if(StandardIDs[1] != "" & StandardIDs[2] == "" ){
Normal <- setdiff(1:dim(collectList)[1],unique(c(ECstd)))
AnalysisType <- "high"
InitList <- list(ECstd,Normal,0)
itType = 1
itTypeCov <- F
}
if(all(StandardIDs[2] != "") & StandardIDs[1] == ""){
Normal <- setdiff(1:dim(collectList)[1],unique(c(BSA)))
AnalysisType <- "low"
InitList <- list(0,Normal,BSA)
itType = 3
itTypeCov <- T
}
if(all(StandardIDs == "")){
Normal <-1:dim(collectList)[1]
AnalysisType <- "none"
InitList <- list(0,Normal,0)
itType = 2
itTypeCov <- F
}
#InitList <<- InitList
collectListAll <- list()
collectListLife <- list()
if(Machines == "NA"|all(Machines== "") ){
Names <- grepRE(as.character(collectList$Name),RESettings$REmac)
Machines = unique(Names)
}else{Machines = Machines}
if(!exists("funlastLoop", envir = .GlobalEnv)){funlastLoop <<- 2}
if(funlastLoop %% 10 == 0| funlastLoop == 2){
# BSA <<- BSA
# ECstd <<- ECstd
# Normal <<- Normal
if(AnalysisType == "both"|AnalysisType == "high" ){
try({CompareMachines(collectList[ECstd,],paste(finalMQQC,"TimeLines","MachineComparisonHighComplexStd.pdf",sep = "/"),FilterMachines = Machines)})
try({CompareMachines(collectList[BSA,],paste(finalMQQC,"TimeLines","MachineComparisonLowComplexStd.pdf",sep = "/"),FilterMachines = Machines)})
quanDir <- paste(folder,"_RmqqcFile_Quantiles",sep = "/")
dir.create(quanDir,showWarnings = F)
# LoadSettings(tempListOne = collectList[ECstd,],collectList= collectList,ECstd=ECstd,RESettings = RESettings,finalMQQC = finalMQQC, PDFname = "ComplexStandardComparison.pdf", TargetVec = StandardIDs[1],PDF = T, Machines = Machines,StandardIDs = StandardIDs)
try(ECquan <- CompareComplexStdFromTable(tempListOne = collectList[ECstd,],RESettings = RESettings,finalMQQC = finalMQQC, PDFname = "ComplexStandardComparison.pdf", TargetVec = StandardIDs[1],PDF = T, Machines = Machines,StandardIDs = StandardIDs),silent = T)
if(exists("ECquan")){
Quan <- NA
try(Quan <- ECquan)
try(save(Quan,file = paste(quanDir,paste(StandardIDs[1],"quan.rda",sep = "_"),sep = "/"),precheck = F),silent = T)
}
# LoadSettings(AllData = collectList,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = T, RESettings = RESettings,TLname= "-high")
try(plottingTimeLineFunction(AllData = collectList[ECstd,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = T, RESettings = RESettings,TLname= "-high",pdfShow = F),silent = F)
try(trash <-CompareComplexStdFromTable(collectList[ECstd,],RESettings,F,finalMQQC, PDFname = "ComplexStandardComparison.jpg", TargetVec = StandardIDs[1],PDF = F, Machines = Machines),silent = T)
try(plottingTimeLineFunction(AllData = collectList[ECstd,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = F, RESettings = RESettings,TLname= "-high"),silent = T)
}
if(AnalysisType == "both"|AnalysisType =="low"){
try({CompareMachines(collectList[BSA,],paste(finalMQQC,"TimeLines","MachineComparisonLowComplexStd.pdf",sep = "/"))})
try(BSAquan<- CompareComplexStdFromTable(collectList[BSA,],RESettings,F,finalMQQC, PDFname = "LowComplexStandardComparison.pdf", TargetVec = StandardIDs[2],PDF = T, Machines = Machines),silent = T)
# try(save(BSAquan,file = paste(quanDir,"BSAquan.rda",sep = "/")),silent = T)
if(exists("BSAquan")){
Quan <- NA
try(Quan <- BSAquan)
try(save(Quan,file = paste(quanDir,paste(StandardIDs[2],"quan.rda",sep = "_"),sep = "/")),silent = T)
}
try(plottingTimeLineFunction(AllData = collectList[BSA,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = T, RESettings = RESettings,TLname= "-Low"),silent = T)
try(plottingTimeLineFunction(AllData = collectList[BSA,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = F, RESettings = RESettings,TLname= "-Low"),silent = T)
try(Trash <- CompareComplexStdFromTable(collectList[BSA,],RESettings,F,finalMQQC, PDFname = "LowComplexStandardComparison.jpg", TargetVec = "BSA",PDF = F, Machines = Machines),silent = T)
}
if(length(Normal) > 0){
try(RestQuan <- CompareComplexStdFromTable(collectList[Normal,],RESettings,F,finalMQQC, PDFname = "NormalSampleComparison.pdf",main = "MQQC Normal Samples Parameter Comparison", TargetVec = "",PDF = T, Machines = Machines),silent = T)
try(Trash <- CompareComplexStdFromTable(collectList[Normal,],RESettings,F,finalMQQC, PDFname = "NormalSampleComparison.jpg",main = "MQQC Normal Samples Parameter Comparison", TargetVec = "",PDF = F, Machines = Machines),silent = T)
try(plottingTimeLineFunction(AllData = collectList[Normal,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = T, RESettings = RESettings, TLname= "-All"),silent = T)
try(plottingTimeLineFunction(AllData = collectList[Normal,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = F, RESettings = RESettings, TLname= "-All"),silent = T)
if(exists("RestQuan")){
Quan <- NA
try(Quan <- RestQuan)
try(save(Quan,file = paste(quanDir,"AllQuan.rda",sep = "/")),silent = T)
}
}
}
it <<- 1
collectList$SourceTime[is.na(collectList$SourceTime)] <- collectList$System.Time.s[is.na(collectList$SourceTime)]
for(iList in InitList){
tempListOne <- collectList[iList,]
collectListSorted <- c()
collectListSortedLife <- c()
#RE work TODO
#Names <- sapply(strsplit(tempListOne$Name,"_"),function(x){x[1]})
if(dim(tempListOne)[1] != 0){
Names <- grepRE(as.character(tempListOne$Name),RESettings$REmac)
# Fix, cause crash, if NA in Names
Names[is.na(Names)] <- ""
#NamesUni <- unique(Names)
for(iNames in unique(Names)){
tempList <- tempListOne[Names == iNames,]
tempList <- tempList[!is.na(tempList$SourceTime),]
# cat("\r",iNames,dim(tempList))
if(ordertype == "source"){
try( tempList <- tempList[order(as.numeric(tempList$SourceTime),decreasing = T),])
}
if(ordertype == "system"){
try( tempList <- tempList[order(as.numeric(tempList$System.Time.s),decreasing = T),])
}
if(dim(tempList)[1] > maxReport){
tempList <- tempList[1:maxReport,]
}
if(any(iNames==Machines)
#&!all(is.na(tempList[1,]))
){
collectListSortedLife <- rbind(collectListSortedLife,tempList[1,])
if(it == itType){
if(itTypeCov){
linkInput <- tempList$Coverage[1]
HotLinkType = "Coverage"
}else{
linkInput <- tempList$msms.count[1]
HotLinkType = "msms/min"
}
HotLink[iNames==Machines] <- linkInput
HotLinkPath[iNames == Machines] <- paste(".",htmlPdfFold,basename(gsub(".csv$",".pdf", tempList$exitPath)),sep = "/")
HotLinkCol[iNames==Machines] <- tempList$TotalScoreColor.Total[1]
days <- abs(as.numeric(tempList$System.Time.s)-as.numeric(Sys.time()))/(60*60*24)
# tempList <<- tempList
if(!is.na(days)){
if(days > dayThresh){
HotLinkCol[iNames==Machines] <- "#797979"
}
}
FCheck <-file.copy(gsub("csv$","pdf",tempList$exitPath[1]),paste(finalMQQC, StandardIDs[1],paste(iNames,".pdf",sep = ""),sep = "/"), overwrite = T)
}else{
FCheck <- file.copy(gsub("csv$","pdf",tempList$exitPath[1]),paste(finalMQQC,"all",paste(iNames,".pdf",sep = ""),sep = "/"),overwrite = T)
}
}
if(!all(is.na(tempList))){
collectListSorted <- rbind(collectListSorted,tempList)
}
}
collectListAll[[it]] <- collectListSorted
collectListLife[[it]] <- collectListSortedLife
#Prepare for HTML
tempInput <- as.character(collectListSorted$Name)
if(length(tempInput) ==0){tempInput <- "NO DATA"}
temp <- stringSplitter(tempInput,RESettings = RESettings)
if(is.vector(temp)){temp <- as.matrix(temp)}
if(dim(temp)[2] == 5){
temp[,5] <- substr(temp[,5],start = 1,stop = 20)
input <- temp
input <- apply(input,2,function(x){gsub(RESettingsSep,"",x,fixed = T)})
colsTemp <- c("MS","Time","User","Species","misc")
}else{
input <- as.character(collectListSorted$Name)
colsTemp <- c("Sample")
}
## ColorCodeScore
colorCode <- collectListSorted$TotalScoreColor.Total
colorCode <- paste("<font color = '",colorCode,"'>♥</font>",sep = "")
TotalScore <- round(as.numeric(as.character(collectListSorted$TotalScore.Total))*100)
#TotalScore[is.na(TotalScore)] <- 0
TotalScore[is.na(TotalScore)] <- 0
ncharL <- 3- nchar(TotalScore)
TotalScoreAdd <- sapply(ncharL,function(x){
if(x !=0){
x <- paste(rep(0,abs(x)),collapse = "")
return(x)
}else{return("")}
})
TotalScore <- paste(TotalScoreAdd ,TotalScore,sep = "")
colorCode <- paste(TotalScore,colorCode)
pathPdf <- gsub(".csv$",".pdf",collectListSorted$exitPath)
pathDepPepPie <- gsub(".csv$",".pdf",collectListSorted$exitPath)
pathDepPepPie <- paste(dirname(pathDepPepPie),paste("DepPepPie_",basename(pathDepPepPie),sep = ""),sep = "/")
pathDepPepPie <- gsub("raw.pdf$","pdf", pathDepPepPie)
# Same for chromatogram
pathChrom <- gsub(".csv$",".pdf",collectListSorted$exitPath)
pathChrom <- paste(dirname(pathChrom),paste("chromatogram_",basename(pathChrom),sep = ""),sep = "/")
pathChrom <- gsub("raw.pdf$","pdf", pathChrom)
pathMSF <- pathChrom#gsub("^chromatogram_","MSF_",pathChrom)
pathMSF <- paste(dirname(pathMSF),gsub("^chromatogram_","MSF_",basename(pathMSF)),sep ="/")
pathRP <- pathChrom
pathRP <- paste(dirname(pathRP),gsub("^chromatogram_","RetPlots_",basename(pathRP)),sep ="/")
pathPdf <- gsub(".RAW_folder/","RAW_folder/",pathPdf) # !!!! Temporal Solution, folder is written without ".", should be better fixed while folder is written
###
# function to move pdf to html Output
###
# move all Files:
ActualFile <- list.files(paste(finalMQQC,htmlPdfFold,sep = "/"))
ToMove <- setdiff(basename(pathPdf),ActualFile)
if(length(ToMove) > 0){
ToMove <- merge.control(basename(unique(pathPdf)),ToMove)
ToMove <- unique(pathPdf)[ToMove]
if(any(!file.exists(dirname(ToMove)))){
FixedPath <- sapply(strsplit(ToMove,paste(sucFolder,"/",sep = ""),fixed = T),function(x){
# x <<- x
return(paste(folder,sucFolder,x[2],sep = "/"))
})
ToMove <- FixedPath
}
FileExists <- file.exists(ToMove)
if(any(FileExists)){
file.copy(ToMove[FileExists],paste(finalMQQC,htmlPdfFold,basename(ToMove)[FileExists],sep = "/"))
}
#ToMove <- grep("BSAdp",ToMove,value = T)
if(any(!FileExists) ){
ToMove <- ToMove#[!FileExists]
ToMove <- paste(gsub("_folder$","raw_folder",dirname(ToMove)),basename(ToMove),sep = "/")
FileExists <- file.exists(ToMove)
if(any(FileExists)){
file.copy(ToMove[FileExists],paste(finalMQQC,htmlPdfFold,basename(ToMove)[FileExists],sep = "/"))
}
ToMove <- ToMove[FileExists]
}
### Move PDFs Types
#file.copy(ToMove,paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/"))
if(length(ToMove) > 0){
ToMoveInit <- ToMove
ToMove <- paste(dirname(ToMoveInit),paste("MSMS_Dens_",basename(ToMoveInit),sep = ""),sep = "/")
ToMove <- gsub("raw.pdf$","pdf", ToMove)
try(Fcheck <- file.copy(ToMove, paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/")))
ToMove <- paste(dirname(ToMoveInit),paste("DepPepPie_",basename(ToMoveInit),sep = ""),sep = "/")
ToMove <- gsub("raw.pdf$","pdf", ToMove)
try(Dcheck <- file.copy(ToMove,paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/"),overwrite = T))
ToMove <- paste(dirname(ToMoveInit),paste("chromatogram_",basename(ToMoveInit),sep = ""),sep = "/")
ToMove <- gsub("raw.pdf$","pdf", ToMove)
try(Ccheck <- file.copy(ToMove, paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/"),overwrite = T))
ToMove <- paste(dirname(ToMoveInit),paste("MSF_",basename(ToMoveInit),sep = ""),sep = "/")
ToMove <- gsub("raw.pdf$","pdf", ToMove)
try(Ccheck <- file.copy(ToMove, paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/"),overwrite = T))
ToMove <- paste(dirname(ToMoveInit),paste("RetPlots_",basename(ToMoveInit),sep = ""),sep = "/")
ToMove <- gsub("raw.pdf$","pdf", ToMove)
try(Ccheck <- file.copy(ToMove, paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/"),overwrite = T))
}
}
# Make Relative Paths:
tempPaths <- paste(".",htmlPdfFold,basename(pathPdf),sep = "/")
tempPathsDepPepPie2 <- paste(".", htmlPdfFold,basename(pathDepPepPie),sep = "/")
pathChrom2 <- paste(".", htmlPdfFold,basename(pathChrom),sep = "/")
pathMSF2 <- paste(".", htmlPdfFold,basename(pathMSF),sep = "/")
pathRP2 <- paste(".", htmlPdfFold,basename(pathRP),sep = "/")
#if(exists("Fcheck")){
#tempPaths[!file.exists(pathPdf)] <- ""
#tempPathsDepPepPie2[!file.exists(pathDepPepPie)] <- ""
#pathChrom2[!file.exists(pathChrom)] <- ""
#}
collectListSorted$System.Time <- substr(collectListSorted$System.Time,2,nchar(as.character(collectListSorted$System.Time)))
substr(collectListSorted$System.Time , 11, 12) <- " "
if(length(pathPdf) >0){
#tempPathsMsMs <-as.vector(as.matrix(tempPaths)[2,])
tempPaths <- tempPaths
tempPathsLog <- file.exists(Hui <- paste(finalMQQC,gsub("^./","",tempPaths),sep = "/"))
tempPaths <- paste("<a href ='", tempPaths,"' target ='_blank' >QC</a>",sep = "")
tempPaths[!tempPathsLog] <- ""
#tempPaths[!tempPathsLog] <- ""
# DP pie paths
tempPathsDepPepPie2 <- tempPathsDepPepPie2
tempPathsDepPepPie2Log <-file.exists(paste(finalMQQC,gsub("^./","",tempPathsDepPepPie2),sep = "/"))
tempPathsDepPepPie2 <- paste("<a href ='", tempPathsDepPepPie2,"' target ='_blank' >MD</a>",sep = "")
tempPathsDepPepPie2[!tempPathsDepPepPie2Log] <- ""
pathMSF2 <- pathMSF2
pathMSF2Log <-file.exists(paste(finalMQQC,gsub("^./","",pathMSF2),sep = "/"))
pathMSF2 <- paste("<a href ='", pathMSF2,"' target ='_blank' >MD</a>",sep = "")
pathMSF2[!pathMSF2Log] <- ""
# Chromatogram Paths
paste(finalMQQC,"files",sep = "/")
pathChrom2Log <- file.exists(paste(finalMQQC,gsub("^./","",pathChrom2),sep = "/"))
tempPathsChrom2 <- paste("<a href ='", pathChrom2,"' target ='_blank' >CH</a>",sep = "")
tempPathsChrom2[!pathChrom2Log] <- ""
collectListSorted <- as.data.frame(collectListSorted)
colnames(collectListSorted) <- make.names(colnames(collectListSorted))
tempsel <- grep("Coverage",colnames(collectListSorted))[1]
tempsel <- tempsel[!is.na(tempsel)]
CoverageVec <- collectListSorted[tempsel]
if(length(CoverageVec) == 0){CoverageVec <- "NA"}
if(dim(collectListSorted)[1] == 1){
try(collectListSorted <- c( colorCode ,
input,
as.character(collectListSorted$System.Time),
collectListSorted$msms.count,
#collectListSorted$uniPepCount,
round(as.numeric(collectListSorted$quan.msms.min),2) ,
round(as.numeric(collectListSorted$mass.error.uncal.50.),2),
collectListSorted$score.50.,
CoverageVec,
tempPaths,
tempPathsChrom2,
pathMSF2))
collectListSorted <- as.data.frame(collectListSorted)
}else{
try(collectListSorted <- cbind( colorCode ,
input,
as.character(collectListSorted$System.Time),
collectListSorted$msms.count,
#collectListSorted$uniPepCount,
round(as.numeric(collectListSorted$quan.msms.min),2) ,
round(as.numeric(collectListSorted$mass.error.uncal.50.),2),
collectListSorted$score.50.,
CoverageVec,
tempPaths,
tempPathsChrom2,
pathMSF2))
}
try(colnames(collectListSorted) <- c("",colsTemp,"Time","Peptides","MSMS/min","mass_error_[ppm]","Score_M","Coverage","QC","Chrom","MD"))
alignVec <- c("center","left",rep("center",(dim(collectListSorted)[2]-2)))
#collectListSorted <- collectListSorted[order(collectListSorted[,7]),]
names(collectListSorted)[is.na(names(collectListSorted))] <- "..."
collectListSorted <- collectListSorted[!is.na(collectListSorted$MS),]
if(length(collectListSorted) == 0){collectListSorted <- matrix(c(rep("NO DATA",length(alignVec))),byrow = T,1)}
if(it ==1){
try(tableHtml2 <-HtmlTable(c2<- collectListSorted[hum<-!apply(collectListSorted,2,function(x){all(is.na(x))})], tableDesign = "table-design2"))
if(!exists("tableHtml2")){tableHtml2 <- NULL}
}
if(it ==2){
try(tableHtml <- HtmlTable(c1<-collectListSorted[!apply(collectListSorted,2,function(x){all(is.na(x))})], tableDesign = "table-design"))
if(!exists("tableHtml")){tableHtml <- NULL}
}
if(it ==3){
try(tableHtml3 <-HtmlTable(c3<-collectListSorted[!apply(collectListSorted,2,function(x){all(is.na(x))})], tableDesign = "table-design3"))
if(!exists("tableHtml3")){tableHtml3 <- NULL}
}
}else{
if(it == 1){
tableHtml2 <- ""
}else{ tableHtml <- ""}
if(it == 3){
tableHtml3 <- ""
}
}
}
#####
paste(finalMQQC,"all",paste(Machines,".pdf",sep = ""),sep = "/")
insertText <- list.files(finalMQQC,pattern = "insertText.txt",full.name = T)
if(length(insertText) > 0){
insertText <- paste(readLines(insertText),collapse = "\n")
}else{
insertText = ""
}
it <- it+1
}
# tableHtml2 <<- tableHtml2
if(!exists("tableHtml")){tableHtml <- "NO DATA"}
if(!exists("tableHtml2")){tableHtml2 <- "NO DATA"}
if(!exists("tableHtml3")){tableHtml3 <- "NO DATA"}
#tableHtml <<- tableHtml # EC
#tableHtml2 <<- tableHtml2 # sample data
#tableHtml3 <<- tableHtml3 # BSA
if(all(Machines == "NA")){
MachinesUsed = unique(collectListSorted$MS)
}else{MachinesUsed = Machines}
try(writeToHtml(inputVec = sort(paste(".", StandardIDs[1],paste(Machines,".pdf",sep = ""),sep = "/")),inputVec2 = sort(paste(".","all",paste(Machines,".pdf",sep = ""),sep = "/")),path = paste(finalMQQC,"index.html",sep = "/"),Table = tableHtml,Table2 = tableHtml2 ,Table3 = tableHtml3, insertText = insertText,Machines = MachinesUsed, StandardIDs = StandardIDs))
try(htmlMod(pathHtml = paste(finalMQQC,"index.html",sep = "/"),Machines = MachinesUsed,Counts = HotLink,BGcolor =as.character(HotLinkCol),pdfPaths = HotLinkPath,Type = HotLinkType))
}
cat("\rfinished FUNFINAL function")
}
#
# library(mqqc)
# if(!exists("Param")){
# Param <- mqqcGUI()
# folder <- Param$folder
# RESettings <- Param[grep("^RE",names(Param))]
# StandardIDs = c("","");placeholder = "PLACEHOLDER"
# LoadSettings(withinlastyear = T,maxReport = 10,sucFolder="_RmqqcFile_Processed",StandardIDs = c("HSstd","BSA"),finalMQQC=Param$htmloutPath,folder =Param$folder, RESettings = RESettings,Machines = Param$Machines,dayThresh = 5, RESettingsSep = "_",ordertype = "system")
# LoadSettings(RESettingsSep = "_", placeholder = "PLACEHOLDER" )
# funlastLoop = 2
# finalMQQC <- Param$htmloutPath
# htmloutPath <- Param$htmloutPath
# }
# try( FUNFINAL(finalMQQC=htmloutPath,folder =folder,sucFolder = sucFolder, RESettings = RESettings, Machines = Param$Machines, StandardIDs = StandardIDs,ordertype = "source",maxReport = Param$ListLength))
# system(paste("open ", paste(finalMQQC,"index.html",sep = "/"),sep = ""))
#finalMQQC <- finalMQQC
#sucFolder="_RmqqcFile_Processed"
# try( FUNFINAL(finalMQQC="/Users/henno/temp/mqqc/_RmqqcFile_html/",folder ="/Users/henno/temp/mqqc/",sucFolder = "/Users/henno/temp/mqqc/_RmqqcFile_Processed/", RESettings = RESettings, Machines = c("Anakin","Gonzo","Animal"), StandardIDs = StandardIDs,ordertype = "source",maxReport = Param$ListLength))
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mqqc documentation built on July 30, 2020, 3 p.m.
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Defines functions FUNFINAL
FUNFINAL <-
function(finalMQQC = "D:/resultsmqqc",folder,sucFolder="_RmqqcFile_Processed",Machines = c("Bibo","Kermit","Grobi","Bert","Tiffy"), dayThresh = 5, RESettings = NULL, RESettingsSep = "_",StandardIDs = c("ECstd","BSA"), placeholder = "PLACEHOLDER" ,ordertype = "source",withinlastyear = T,maxReport = 10){
#StandardIDs[1] = ""
# ToDo Table is not rpeorted # html Path is not set
htmlPdfFold <- "files"
dir.create(finalMQQC, showWarnings = F)
dir.create(allPath <- paste(finalMQQC,"all",sep = "/"), showWarnings = F)
dir.create(ECstdPath <- paste(finalMQQC, StandardIDs[2],sep = "/"), showWarnings = F)
dir.create(ECstdPath <- paste(finalMQQC,"files",sep = "/"), showWarnings = F)
dir.create(paste(finalMQQC ,"TimeLines",sep = "/"),showWarnings = F)
if(length(list.files(finalMQQC,pattern = "example.css",recursive = T))== 0){
unzip(list.files(paste(path.package("mqqc"),"data/",sep = "/"),full.name = T,pattern = "html.zip"),exdir = finalMQQC)
}
HotLink = rep("-",length(Machines))
HotLinkCol = rep("#ffffff",length(Machines))
HotLinkPath = rep("-",length(Machines))
collectListPath <- paste(folder,sucFolder,"list_collect.sqlite",sep = "/")
if(file.exists(collectListPath)){
collectList <- dbreadfile(collectListPath)
}
if(length(collectList) > 0){
# collectList <- read.csv(collectListPath, check.names = F,stringsAsFactors = F)
# collectList <- dbreadfile(collectListPath)
collectList <- collectList[!is.na(collectList$Name),]
if(withinlastyear){
yeard <- max(as.numeric(as.character(collectList$System.Time.s)),na.rm = T)-31536000
collectList$System.Time.s[is.na(collectList$System.Time.s)] <- 0
collectList <- collectList[as.numeric(as.character(collectList$System.Time.s)) > yeard,]
}
collectList <- collectList[!is.na(collectList$msms.count),]
collectList <- cbind(1:dim(collectList)[1],collectList)
collectList <- collectList[!duplicated(collectList$Name),]
Names <- collectList$Name
#RE work TODO
if(length(grep(placeholder,RESettings$REpar)) > 0){
StandardIDsRE <- sapply(StandardIDs ,function(x){gsub(placeholder,x,RESettings$REpar)})
# try(StandardIDsRE <- gsub(paste(RESettingsSep,"$",sep = ""),"", StandardIDsRE))
ECstd <- grep(StandardIDsRE[1],collectList$Name,ignore.case = T)
BSA <- grep(StandardIDsRE[2],collectList$Name,ignore.case = T)
}else{
TempNames <- grepRE( gsub(".raw","_raw",collectList$Name),"\\D*_\\d*_[^_]*_[^_]*")
TempNames <- sapply(strsplit(as.character(TempNames),"_"),function(x){x[length(x)]})
ECstd <- 1:dim(collectList)[1]
ECstd <- ECstd[TempNames == StandardIDsRE[1]]
BSA <- 1:dim(collectList)[1]
BSA <- BSA[TempNames == StandardIDsRE[2]]
}
if(all(StandardIDs != "")){
Normal <- setdiff(1:dim(collectList)[1],unique(c(ECstd,BSA)))
AnalysisType <- "both"
InitList <- list(ECstd,Normal, BSA)
itType = 1
itTypeCov <- F
}
if(StandardIDs[1] != "" & StandardIDs[2] == "" ){
Normal <- setdiff(1:dim(collectList)[1],unique(c(ECstd)))
AnalysisType <- "high"
InitList <- list(ECstd,Normal,0)
itType = 1
itTypeCov <- F
}
if(all(StandardIDs[2] != "") & StandardIDs[1] == ""){
Normal <- setdiff(1:dim(collectList)[1],unique(c(BSA)))
AnalysisType <- "low"
InitList <- list(0,Normal,BSA)
itType = 3
itTypeCov <- T
}
if(all(StandardIDs == "")){
Normal <-1:dim(collectList)[1]
AnalysisType <- "none"
InitList <- list(0,Normal,0)
itType = 2
itTypeCov <- F
}
#InitList <<- InitList
collectListAll <- list()
collectListLife <- list()
if(Machines == "NA"|all(Machines== "") ){
Names <- grepRE(as.character(collectList$Name),RESettings$REmac)
Machines = unique(Names)
}else{Machines = Machines}
if(!exists("funlastLoop", envir = .GlobalEnv)){funlastLoop <<- 2}
if(funlastLoop %% 10 == 0| funlastLoop == 2){
# BSA <<- BSA
# ECstd <<- ECstd
# Normal <<- Normal
if(AnalysisType == "both"|AnalysisType == "high" ){
try({CompareMachines(collectList[ECstd,],paste(finalMQQC,"TimeLines","MachineComparisonHighComplexStd.pdf",sep = "/"),FilterMachines = Machines)})
try({CompareMachines(collectList[BSA,],paste(finalMQQC,"TimeLines","MachineComparisonLowComplexStd.pdf",sep = "/"),FilterMachines = Machines)})
quanDir <- paste(folder,"_RmqqcFile_Quantiles",sep = "/")
dir.create(quanDir,showWarnings = F)
# LoadSettings(tempListOne = collectList[ECstd,],collectList= collectList,ECstd=ECstd,RESettings = RESettings,finalMQQC = finalMQQC, PDFname = "ComplexStandardComparison.pdf", TargetVec = StandardIDs[1],PDF = T, Machines = Machines,StandardIDs = StandardIDs)
try(ECquan <- CompareComplexStdFromTable(tempListOne = collectList[ECstd,],RESettings = RESettings,finalMQQC = finalMQQC, PDFname = "ComplexStandardComparison.pdf", TargetVec = StandardIDs[1],PDF = T, Machines = Machines,StandardIDs = StandardIDs),silent = T)
if(exists("ECquan")){
Quan <- NA
try(Quan <- ECquan)
try(save(Quan,file = paste(quanDir,paste(StandardIDs[1],"quan.rda",sep = "_"),sep = "/"),precheck = F),silent = T)
}
# LoadSettings(AllData = collectList,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = T, RESettings = RESettings,TLname= "-high")
try(plottingTimeLineFunction(AllData = collectList[ECstd,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = T, RESettings = RESettings,TLname= "-high",pdfShow = F),silent = F)
try(trash <-CompareComplexStdFromTable(collectList[ECstd,],RESettings,F,finalMQQC, PDFname = "ComplexStandardComparison.jpg", TargetVec = StandardIDs[1],PDF = F, Machines = Machines),silent = T)
try(plottingTimeLineFunction(AllData = collectList[ECstd,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = F, RESettings = RESettings,TLname= "-high"),silent = T)
}
if(AnalysisType == "both"|AnalysisType =="low"){
try({CompareMachines(collectList[BSA,],paste(finalMQQC,"TimeLines","MachineComparisonLowComplexStd.pdf",sep = "/"))})
try(BSAquan<- CompareComplexStdFromTable(collectList[BSA,],RESettings,F,finalMQQC, PDFname = "LowComplexStandardComparison.pdf", TargetVec = StandardIDs[2],PDF = T, Machines = Machines),silent = T)
# try(save(BSAquan,file = paste(quanDir,"BSAquan.rda",sep = "/")),silent = T)
if(exists("BSAquan")){
Quan <- NA
try(Quan <- BSAquan)
try(save(Quan,file = paste(quanDir,paste(StandardIDs[2],"quan.rda",sep = "_"),sep = "/")),silent = T)
}
try(plottingTimeLineFunction(AllData = collectList[BSA,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = T, RESettings = RESettings,TLname= "-Low"),silent = T)
try(plottingTimeLineFunction(AllData = collectList[BSA,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = F, RESettings = RESettings,TLname= "-Low"),silent = T)
try(Trash <- CompareComplexStdFromTable(collectList[BSA,],RESettings,F,finalMQQC, PDFname = "LowComplexStandardComparison.jpg", TargetVec = "BSA",PDF = F, Machines = Machines),silent = T)
}
if(length(Normal) > 0){
try(RestQuan <- CompareComplexStdFromTable(collectList[Normal,],RESettings,F,finalMQQC, PDFname = "NormalSampleComparison.pdf",main = "MQQC Normal Samples Parameter Comparison", TargetVec = "",PDF = T, Machines = Machines),silent = T)
try(Trash <- CompareComplexStdFromTable(collectList[Normal,],RESettings,F,finalMQQC, PDFname = "NormalSampleComparison.jpg",main = "MQQC Normal Samples Parameter Comparison", TargetVec = "",PDF = F, Machines = Machines),silent = T)
try(plottingTimeLineFunction(AllData = collectList[Normal,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = T, RESettings = RESettings, TLname= "-All"),silent = T)
try(plottingTimeLineFunction(AllData = collectList[Normal,],folder=folder,finalMQQC = finalMQQC, TargetVec = StandardIDs[1],PDF = F, RESettings = RESettings, TLname= "-All"),silent = T)
if(exists("RestQuan")){
Quan <- NA
try(Quan <- RestQuan)
try(save(Quan,file = paste(quanDir,"AllQuan.rda",sep = "/")),silent = T)
}
}
}
it <<- 1
collectList$SourceTime[is.na(collectList$SourceTime)] <- collectList$System.Time.s[is.na(collectList$SourceTime)]
for(iList in InitList){
tempListOne <- collectList[iList,]
collectListSorted <- c()
collectListSortedLife <- c()
#RE work TODO
#Names <- sapply(strsplit(tempListOne$Name,"_"),function(x){x[1]})
if(dim(tempListOne)[1] != 0){
Names <- grepRE(as.character(tempListOne$Name),RESettings$REmac)
# Fix, cause crash, if NA in Names
Names[is.na(Names)] <- ""
#NamesUni <- unique(Names)
for(iNames in unique(Names)){
tempList <- tempListOne[Names == iNames,]
tempList <- tempList[!is.na(tempList$SourceTime),]
# cat("\r",iNames,dim(tempList))
if(ordertype == "source"){
try( tempList <- tempList[order(as.numeric(tempList$SourceTime),decreasing = T),])
}
if(ordertype == "system"){
try( tempList <- tempList[order(as.numeric(tempList$System.Time.s),decreasing = T),])
}
if(dim(tempList)[1] > maxReport){
tempList <- tempList[1:maxReport,]
}
if(any(iNames==Machines)
#&!all(is.na(tempList[1,]))
){
collectListSortedLife <- rbind(collectListSortedLife,tempList[1,])
if(it == itType){
if(itTypeCov){
linkInput <- tempList$Coverage[1]
HotLinkType = "Coverage"
}else{
linkInput <- tempList$msms.count[1]
HotLinkType = "msms/min"
}
HotLink[iNames==Machines] <- linkInput
HotLinkPath[iNames == Machines] <- paste(".",htmlPdfFold,basename(gsub(".csv$",".pdf", tempList$exitPath)),sep = "/")
HotLinkCol[iNames==Machines] <- tempList$TotalScoreColor.Total[1]
days <- abs(as.numeric(tempList$System.Time.s)-as.numeric(Sys.time()))/(60*60*24)
# tempList <<- tempList
if(!is.na(days)){
if(days > dayThresh){
HotLinkCol[iNames==Machines] <- "#797979"
}
}
FCheck <-file.copy(gsub("csv$","pdf",tempList$exitPath[1]),paste(finalMQQC, StandardIDs[1],paste(iNames,".pdf",sep = ""),sep = "/"), overwrite = T)
}else{
FCheck <- file.copy(gsub("csv$","pdf",tempList$exitPath[1]),paste(finalMQQC,"all",paste(iNames,".pdf",sep = ""),sep = "/"),overwrite = T)
}
}
if(!all(is.na(tempList))){
collectListSorted <- rbind(collectListSorted,tempList)
}
}
collectListAll[[it]] <- collectListSorted
collectListLife[[it]] <- collectListSortedLife
#Prepare for HTML
tempInput <- as.character(collectListSorted$Name)
if(length(tempInput) ==0){tempInput <- "NO DATA"}
temp <- stringSplitter(tempInput,RESettings = RESettings)
if(is.vector(temp)){temp <- as.matrix(temp)}
if(dim(temp)[2] == 5){
temp[,5] <- substr(temp[,5],start = 1,stop = 20)
input <- temp
input <- apply(input,2,function(x){gsub(RESettingsSep,"",x,fixed = T)})
colsTemp <- c("MS","Time","User","Species","misc")
}else{
input <- as.character(collectListSorted$Name)
colsTemp <- c("Sample")
}
## ColorCodeScore
colorCode <- collectListSorted$TotalScoreColor.Total
colorCode <- paste("<font color = '",colorCode,"'>♥</font>",sep = "")
TotalScore <- round(as.numeric(as.character(collectListSorted$TotalScore.Total))*100)
#TotalScore[is.na(TotalScore)] <- 0
TotalScore[is.na(TotalScore)] <- 0
ncharL <- 3- nchar(TotalScore)
TotalScoreAdd <- sapply(ncharL,function(x){
if(x !=0){
x <- paste(rep(0,abs(x)),collapse = "")
return(x)
}else{return("")}
})
TotalScore <- paste(TotalScoreAdd ,TotalScore,sep = "")
colorCode <- paste(TotalScore,colorCode)
pathPdf <- gsub(".csv$",".pdf",collectListSorted$exitPath)
pathDepPepPie <- gsub(".csv$",".pdf",collectListSorted$exitPath)
pathDepPepPie <- paste(dirname(pathDepPepPie),paste("DepPepPie_",basename(pathDepPepPie),sep = ""),sep = "/")
pathDepPepPie <- gsub("raw.pdf$","pdf", pathDepPepPie)
# Same for chromatogram
pathChrom <- gsub(".csv$",".pdf",collectListSorted$exitPath)
pathChrom <- paste(dirname(pathChrom),paste("chromatogram_",basename(pathChrom),sep = ""),sep = "/")
pathChrom <- gsub("raw.pdf$","pdf", pathChrom)
pathMSF <- pathChrom#gsub("^chromatogram_","MSF_",pathChrom)
pathMSF <- paste(dirname(pathMSF),gsub("^chromatogram_","MSF_",basename(pathMSF)),sep ="/")
pathRP <- pathChrom
pathRP <- paste(dirname(pathRP),gsub("^chromatogram_","RetPlots_",basename(pathRP)),sep ="/")
pathPdf <- gsub(".RAW_folder/","RAW_folder/",pathPdf) # !!!! Temporal Solution, folder is written without ".", should be better fixed while folder is written
###
# function to move pdf to html Output
###
# move all Files:
ActualFile <- list.files(paste(finalMQQC,htmlPdfFold,sep = "/"))
ToMove <- setdiff(basename(pathPdf),ActualFile)
if(length(ToMove) > 0){
ToMove <- merge.control(basename(unique(pathPdf)),ToMove)
ToMove <- unique(pathPdf)[ToMove]
if(any(!file.exists(dirname(ToMove)))){
FixedPath <- sapply(strsplit(ToMove,paste(sucFolder,"/",sep = ""),fixed = T),function(x){
# x <<- x
return(paste(folder,sucFolder,x[2],sep = "/"))
})
ToMove <- FixedPath
}
FileExists <- file.exists(ToMove)
if(any(FileExists)){
file.copy(ToMove[FileExists],paste(finalMQQC,htmlPdfFold,basename(ToMove)[FileExists],sep = "/"))
}
#ToMove <- grep("BSAdp",ToMove,value = T)
if(any(!FileExists) ){
ToMove <- ToMove#[!FileExists]
ToMove <- paste(gsub("_folder$","raw_folder",dirname(ToMove)),basename(ToMove),sep = "/")
FileExists <- file.exists(ToMove)
if(any(FileExists)){
file.copy(ToMove[FileExists],paste(finalMQQC,htmlPdfFold,basename(ToMove)[FileExists],sep = "/"))
}
ToMove <- ToMove[FileExists]
}
### Move PDFs Types
#file.copy(ToMove,paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/"))
if(length(ToMove) > 0){
ToMoveInit <- ToMove
ToMove <- paste(dirname(ToMoveInit),paste("MSMS_Dens_",basename(ToMoveInit),sep = ""),sep = "/")
ToMove <- gsub("raw.pdf$","pdf", ToMove)
try(Fcheck <- file.copy(ToMove, paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/")))
ToMove <- paste(dirname(ToMoveInit),paste("DepPepPie_",basename(ToMoveInit),sep = ""),sep = "/")
ToMove <- gsub("raw.pdf$","pdf", ToMove)
try(Dcheck <- file.copy(ToMove,paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/"),overwrite = T))
ToMove <- paste(dirname(ToMoveInit),paste("chromatogram_",basename(ToMoveInit),sep = ""),sep = "/")
ToMove <- gsub("raw.pdf$","pdf", ToMove)
try(Ccheck <- file.copy(ToMove, paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/"),overwrite = T))
ToMove <- paste(dirname(ToMoveInit),paste("MSF_",basename(ToMoveInit),sep = ""),sep = "/")
ToMove <- gsub("raw.pdf$","pdf", ToMove)
try(Ccheck <- file.copy(ToMove, paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/"),overwrite = T))
ToMove <- paste(dirname(ToMoveInit),paste("RetPlots_",basename(ToMoveInit),sep = ""),sep = "/")
ToMove <- gsub("raw.pdf$","pdf", ToMove)
try(Ccheck <- file.copy(ToMove, paste(finalMQQC,htmlPdfFold,basename(ToMove),sep = "/"),overwrite = T))
}
}
# Make Relative Paths:
tempPaths <- paste(".",htmlPdfFold,basename(pathPdf),sep = "/")
tempPathsDepPepPie2 <- paste(".", htmlPdfFold,basename(pathDepPepPie),sep = "/")
pathChrom2 <- paste(".", htmlPdfFold,basename(pathChrom),sep = "/")
pathMSF2 <- paste(".", htmlPdfFold,basename(pathMSF),sep = "/")
pathRP2 <- paste(".", htmlPdfFold,basename(pathRP),sep = "/")
#if(exists("Fcheck")){
#tempPaths[!file.exists(pathPdf)] <- ""
#tempPathsDepPepPie2[!file.exists(pathDepPepPie)] <- ""
#pathChrom2[!file.exists(pathChrom)] <- ""
#}
collectListSorted$System.Time <- substr(collectListSorted$System.Time,2,nchar(as.character(collectListSorted$System.Time)))
substr(collectListSorted$System.Time , 11, 12) <- " "
if(length(pathPdf) >0){
#tempPathsMsMs <-as.vector(as.matrix(tempPaths)[2,])
tempPaths <- tempPaths
tempPathsLog <- file.exists(Hui <- paste(finalMQQC,gsub("^./","",tempPaths),sep = "/"))
tempPaths <- paste("<a href ='", tempPaths,"' target ='_blank' >QC</a>",sep = "")
tempPaths[!tempPathsLog] <- ""
#tempPaths[!tempPathsLog] <- ""
# DP pie paths
tempPathsDepPepPie2 <- tempPathsDepPepPie2
tempPathsDepPepPie2Log <-file.exists(paste(finalMQQC,gsub("^./","",tempPathsDepPepPie2),sep = "/"))
tempPathsDepPepPie2 <- paste("<a href ='", tempPathsDepPepPie2,"' target ='_blank' >MD</a>",sep = "")
tempPathsDepPepPie2[!tempPathsDepPepPie2Log] <- ""
pathMSF2 <- pathMSF2
pathMSF2Log <-file.exists(paste(finalMQQC,gsub("^./","",pathMSF2),sep = "/"))
pathMSF2 <- paste("<a href ='", pathMSF2,"' target ='_blank' >MD</a>",sep = "")
pathMSF2[!pathMSF2Log] <- ""
# Chromatogram Paths
paste(finalMQQC,"files",sep = "/")
pathChrom2Log <- file.exists(paste(finalMQQC,gsub("^./","",pathChrom2),sep = "/"))
tempPathsChrom2 <- paste("<a href ='", pathChrom2,"' target ='_blank' >CH</a>",sep = "")
tempPathsChrom2[!pathChrom2Log] <- ""
collectListSorted <- as.data.frame(collectListSorted)
colnames(collectListSorted) <- make.names(colnames(collectListSorted))
tempsel <- grep("Coverage",colnames(collectListSorted))[1]
tempsel <- tempsel[!is.na(tempsel)]
CoverageVec <- collectListSorted[tempsel]
if(length(CoverageVec) == 0){CoverageVec <- "NA"}
if(dim(collectListSorted)[1] == 1){
try(collectListSorted <- c( colorCode ,
input,
as.character(collectListSorted$System.Time),
collectListSorted$msms.count,
#collectListSorted$uniPepCount,
round(as.numeric(collectListSorted$quan.msms.min),2) ,
round(as.numeric(collectListSorted$mass.error.uncal.50.),2),
collectListSorted$score.50.,
CoverageVec,
tempPaths,
tempPathsChrom2,
pathMSF2))
collectListSorted <- as.data.frame(collectListSorted)
}else{
try(collectListSorted <- cbind( colorCode ,
input,
as.character(collectListSorted$System.Time),
collectListSorted$msms.count,
#collectListSorted$uniPepCount,
round(as.numeric(collectListSorted$quan.msms.min),2) ,
round(as.numeric(collectListSorted$mass.error.uncal.50.),2),
collectListSorted$score.50.,
CoverageVec,
tempPaths,
tempPathsChrom2,
pathMSF2))
}
try(colnames(collectListSorted) <- c("",colsTemp,"Time","Peptides","MSMS/min","mass_error_[ppm]","Score_M","Coverage","QC","Chrom","MD"))
alignVec <- c("center","left",rep("center",(dim(collectListSorted)[2]-2)))
#collectListSorted <- collectListSorted[order(collectListSorted[,7]),]
names(collectListSorted)[is.na(names(collectListSorted))] <- "..."
collectListSorted <- collectListSorted[!is.na(collectListSorted$MS),]
if(length(collectListSorted) == 0){collectListSorted <- matrix(c(rep("NO DATA",length(alignVec))),byrow = T,1)}
if(it ==1){
try(tableHtml2 <-HtmlTable(c2<- collectListSorted[hum<-!apply(collectListSorted,2,function(x){all(is.na(x))})], tableDesign = "table-design2"))
if(!exists("tableHtml2")){tableHtml2 <- NULL}
}
if(it ==2){
try(tableHtml <- HtmlTable(c1<-collectListSorted[!apply(collectListSorted,2,function(x){all(is.na(x))})], tableDesign = "table-design"))
if(!exists("tableHtml")){tableHtml <- NULL}
}
if(it ==3){
try(tableHtml3 <-HtmlTable(c3<-collectListSorted[!apply(collectListSorted,2,function(x){all(is.na(x))})], tableDesign = "table-design3"))
if(!exists("tableHtml3")){tableHtml3 <- NULL}
}
}else{
if(it == 1){
tableHtml2 <- ""
}else{ tableHtml <- ""}
if(it == 3){
tableHtml3 <- ""
}
}
}
#####
paste(finalMQQC,"all",paste(Machines,".pdf",sep = ""),sep = "/")
insertText <- list.files(finalMQQC,pattern = "insertText.txt",full.name = T)
if(length(insertText) > 0){
insertText <- paste(readLines(insertText),collapse = "\n")
}else{
insertText = ""
}
it <- it+1
}
# tableHtml2 <<- tableHtml2
if(!exists("tableHtml")){tableHtml <- "NO DATA"}
if(!exists("tableHtml2")){tableHtml2 <- "NO DATA"}
if(!exists("tableHtml3")){tableHtml3 <- "NO DATA"}
#tableHtml <<- tableHtml # EC
#tableHtml2 <<- tableHtml2 # sample data
#tableHtml3 <<- tableHtml3 # BSA
if(all(Machines == "NA")){
MachinesUsed = unique(collectListSorted$MS)
}else{MachinesUsed = Machines}
try(writeToHtml(inputVec = sort(paste(".", StandardIDs[1],paste(Machines,".pdf",sep = ""),sep = "/")),inputVec2 = sort(paste(".","all",paste(Machines,".pdf",sep = ""),sep = "/")),path = paste(finalMQQC,"index.html",sep = "/"),Table = tableHtml,Table2 = tableHtml2 ,Table3 = tableHtml3, insertText = insertText,Machines = MachinesUsed, StandardIDs = StandardIDs))
try(htmlMod(pathHtml = paste(finalMQQC,"index.html",sep = "/"),Machines = MachinesUsed,Counts = HotLink,BGcolor =as.character(HotLinkCol),pdfPaths = HotLinkPath,Type = HotLinkType))
}
cat("\rfinished FUNFINAL function")
}
#
# library(mqqc)
# if(!exists("Param")){
# Param <- mqqcGUI()
# folder <- Param$folder
# RESettings <- Param[grep("^RE",names(Param))]
# StandardIDs = c("","");placeholder = "PLACEHOLDER"
# LoadSettings(withinlastyear = T,maxReport = 10,sucFolder="_RmqqcFile_Processed",StandardIDs = c("HSstd","BSA"),finalMQQC=Param$htmloutPath,folder =Param$folder, RESettings = RESettings,Machines = Param$Machines,dayThresh = 5, RESettingsSep = "_",ordertype = "system")
# LoadSettings(RESettingsSep = "_", placeholder = "PLACEHOLDER" )
# funlastLoop = 2
# finalMQQC <- Param$htmloutPath
# htmloutPath <- Param$htmloutPath
# }
# try( FUNFINAL(finalMQQC=htmloutPath,folder =folder,sucFolder = sucFolder, RESettings = RESettings, Machines = Param$Machines, StandardIDs = StandardIDs,ordertype = "source",maxReport = Param$ListLength))
# system(paste("open ", paste(finalMQQC,"index.html",sep = "/"),sep = ""))
#finalMQQC <- finalMQQC
#sucFolder="_RmqqcFile_Processed"
# try( FUNFINAL(finalMQQC="/Users/henno/temp/mqqc/_RmqqcFile_html/",folder ="/Users/henno/temp/mqqc/",sucFolder = "/Users/henno/temp/mqqc/_RmqqcFile_Processed/", RESettings = RESettings, Machines = c("Anakin","Gonzo","Animal"), StandardIDs = StandardIDs,ordertype = "source",maxReport = Param$ListLength))
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