inst/MetFamily/app_files/server_guiTabInput.R
In ipb-halle/MetFamily: MetFamily: Discovering Regulated Metabolite Families in Untargeted Metabolomics Studies
## data import: fixed parameters
proportionOfMatchingPeaks_ms2PeakGroupDeisotoping <- 0.9
mzDeviationAbsolute_mapping <- 0.01
#minimumNumberOfMS2PeaksPerGroup <- 1
## data
dataList <- NULL
state_tabInput <- reactiveValues(
importedOrLoadedFile_s_ = NULL
)
resetWorkspaceFunctions <- c(resetWorkspaceFunctions, function(){
print("Reset tabInput state")
state_tabInput$importedOrLoadedFile_s_ <<- NULL
})
enableLoadButtons <- function(){
#session$sendCustomMessage("enableButton", "loadProjectData")
#session$sendCustomMessage("enableButton", "loadExampleData")
#session$sendCustomMessage("enableButton", "importMs1Ms2Data")
#session$sendCustomMessage("enableButton", "importMs2Data")
shinyjs::enable("loadProjectData")
shinyjs::enable("loadExampleData")
shinyjs::enable("importMs1Ms2Data")
shinyjs::enable("importMs2Data")
}
disableLoadButtons <- function(){
session$sendCustomMessage("disableButton", "loadProjectData")
session$sendCustomMessage("disableButton", "loadExampleData")
session$sendCustomMessage("disableButton", "importMs1Ms2Data")
session$sendCustomMessage("disableButton", "importMs2Data")
shinyjs::disable("loadProjectData")
shinyjs::disable("loadExampleData")
shinyjs::disable("importMs1Ms2Data")
shinyjs::disable("importMs2Data")
}
obsFile <- observeEvent(input$matrixFile$datapath, {
filePath <- input$matrixFile$datapath
fileName <- input$matrixFile$name
print(paste("Observe file for data", fileName))
if(!is.null(filePath))
shinyjs::enable("loadProjectData")
updateFileInputInfo()
})
obsLoadProjectData <- observeEvent(input$loadProjectData, {
disableLoadButtons()
loadProjectData <- as.numeric(input$loadProjectData)
print(paste("Observe loadProjectData", loadProjectData))
#################################################
## check if button was hit
#if(loadProjectData == loadProjectDataButtonValue)
# return()
#loadProjectDataButtonValue <<- loadProjectData
#################################################
## files
filePath <- input$matrixFile$datapath
loadProjectFile(filePath = filePath)
enableLoadButtons()
})
obsLoadExampleData <- observeEvent(input$loadExampleData, {
disableLoadButtons()
loadExampleData <- as.numeric(input$loadExampleData)
print(paste("Observe loadExampleData", loadExampleData))
#################################################
## check if button was hit
#if(loadExampleData == loadExampleDataButtonValue)
# return()
#loadExampleDataButtonValue <<- loadExampleData
#################################################
## files
filePath <- system.file("extdata/showcase/Project_file_showcase_annotated.csv.gz", package = "MetFamily")
loadProjectFile(filePath = filePath)
enableLoadButtons()
})
loadProjectFile <- function(filePath){
fileName <- basename(filePath)
#########################################################################################
## read data
error <<- NULL
withProgress(message = 'Reading file...', value = 0, {
dataList <<- tryCatch(
{
readClusterDataFromProjectFile(file = filePath, progress = TRUE)
},
error = function(e) {
print(e)
error <<- e
}
)
})
if(!is.null(error)){
print(paste("readClusterDataFromProjectFile resulted in error:", error))
msg <- paste("An error occurred while reading the input files. Please check the file format and content and try again. The error was", error)
output$fileInfo <- renderText({msg})
#session$sendCustomMessage("enableButton", buttonId)
#shinyBS::addPopover(session = session, id = "fileInputSelection", title = "Error", content = "huhu")
msg <- paste(
"An error occurred while reading the input files.",
"Please check the file format and content and try again.",
"The error was:",
"<br>",
error
)
showErrorDialog(msg)
return()
}
print(paste("readClusterDataFromProjectFile finished", dataList$minimumMass))
resetWorkspace()
state_tabInput$importedOrLoadedFile_s_ <<- fileName
updateFileInputInfo()
}
obsImportMs1DataFile <- observeEvent(input$ms1DataFile$datapath, {
fileMs1Path <- input$ms1DataFile$datapath
fileMs1Name <- input$ms1DataFile$name
fileMs2Path <- input$ms2DataFile$datapath
fileMs2Name <- input$ms2DataFile$name
print(paste("Observe import MS1 file", fileMs1Name))
if(all(!is.null(fileMs1Path), !is.null(fileMs2Path)))
shinyjs::enable("importMs1Ms2Data")
else
shinyjs::disable("importMs1Ms2Data")
updateFileInputInfo()
})
obsImportMs2DataFile <- observeEvent(input$ms2DataFile$datapath, {
setImportState()
})
setImportState <- function(){
fileMs1Path <- input$ms1DataFile$datapath
fileMs1Name <- input$ms1DataFile$name
fileMs2Path <- input$ms2DataFile$datapath
fileMs2Name <- input$ms2DataFile$name
print(paste("Observe import MS2 file", fileMs2Name))
if(all(!is.null(fileMs1Path), !is.null(fileMs2Path)))
shinyjs::enable("importMs1Ms2Data")
else
shinyjs::disable("importMs1Ms2Data")
if(!is.null(fileMs2Path))
shinyjs::enable("importMs2Data")
else
shinyjs::disable("importMs2Data")
updateFileInputInfo()
}
obsImportMs1Ms2Data <- observeEvent(input$importMs1Ms2Data, {
disableLoadButtons()
importMs1Ms2Data <- as.numeric(input$importMs1Ms2Data)
print(paste("Observe importMs1Ms2Data", importMs1Ms2Data))
#################################################
## check if button was hit
#if(importMs1Ms2Data == importMs1Ms2DataButtonValue)
# return()
#importMs1Ms2DataButtonValue <<- importMs1Ms2Data
importData(TRUE)
enableLoadButtons()
})
obsImportMs2Data <- observeEvent(input$importMs2Data, {
enableLoadButtons()
importMs2Data <- as.numeric(input$importMs2Data)
print(paste("Observe importMs2Data", importMs2Data))
#################################################
## check if button was hit
#if(importMs2Data == importMs2DataButtonValue)
# return()
#importMs2DataButtonValue <<- importMs2Data
importData(FALSE)
disableLoadButtons()
})
importData <- function(importMS1andMS2data){
#################################################
## files
if(importMS1andMS2data){
fileMs1Path <- input$ms1DataFile$datapath
fileMs1Name <- input$ms1DataFile$name
} else {
fileMs1Path <- NULL
fileMs1Name <- NULL
}
fileMs2Path <- input$ms2DataFile$datapath
fileMs2Name <- input$ms2DataFile$name
#################################################
## params
## project name
projectName <- input$projectName
projectName <- gsub(";", "_", gsub(",", "_", gsub("\t", "_", projectName)))
projectDescription <- input$projectDescription
projectDescription <- gsub(";", "_", gsub(",", "_", gsub("\t", "_", projectDescription)))
## minimum MS2 peak intensity
minimumIntensityOfMaximalMS2peak <- input$minimumIntensityOfMaximalMS2peak
minimumProportionOfMS2peaks <- input$minimumProportionOfMS2peaks
## grouping of MS2 peaks
mzDeviationAbsolute_grouping <- input$mzDeviationAbsolute_grouping
mzDeviationInPPM_grouping <- input$mzDeviationInPPM_grouping
## precursor deisotoping
doPrecursorDeisotoping <- input$doPrecursorDeisotoping
mzDeviationAbsolute_precursorDeisotoping <- input$mzDeviationAbsolute_precursorDeisotoping
mzDeviationInPPM_precursorDeisotoping <- input$mzDeviationInPPM_precursorDeisotoping
maximumRtDifference <- input$maximumRtDifference
## fragment deisotoping
doMs2PeakGroupDeisotoping <- input$doMs2PeakGroupDeisotoping
mzDeviationAbsolute_ms2PeakGroupDeisotoping <- input$mzDeviationAbsolute_ms2PeakGroupDeisotoping
mzDeviationInPPM_ms2PeakGroupDeisotoping <- input$mzDeviationInPPM_ms2PeakGroupDeisotoping
## neutral losses
neutralLossesPrecursorToFragments <- input$neutralLossesPrecursorToFragments
neutralLossesFragmentsToFragments <- input$neutralLossesFragmentsToFragments
#neutralLossesPrecursorToFragments <- TRUE
#neutralLossesFragmentsToFragments <- FALSE
## fixed
proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere <- proportionOfMatchingPeaks_ms2PeakGroupDeisotoping
mzDeviationAbsolute_mappingHere <- mzDeviationAbsolute_mapping
#minimumNumberOfMS2PeaksPerGroupHere <- minimumNumberOfMS2PeaksPerGroup
#################################################
## check params
error <- FALSE
if(any(is.null(minimumIntensityOfMaximalMS2peak), length(minimumIntensityOfMaximalMS2peak) == 0, nchar(minimumIntensityOfMaximalMS2peak) == 0))
error <- TRUE
else{
minimumIntensityOfMaximalMS2peak <- as.numeric(minimumIntensityOfMaximalMS2peak)
error <- error | is.na(minimumIntensityOfMaximalMS2peak)
}
if(any(is.null(minimumProportionOfMS2peaks), length(minimumProportionOfMS2peaks) == 0, nchar(minimumProportionOfMS2peaks) == 0))
error <- TRUE
else{
minimumProportionOfMS2peaks <- as.numeric(minimumProportionOfMS2peaks)
error <- error | is.na(minimumProportionOfMS2peaks)
}
if(any(is.null(mzDeviationAbsolute_grouping), length(mzDeviationAbsolute_grouping) == 0, nchar(mzDeviationAbsolute_grouping) == 0))
error <- TRUE
else{
mzDeviationAbsolute_grouping <- as.numeric(mzDeviationAbsolute_grouping)
error <- error | is.na(mzDeviationAbsolute_grouping)
}
if(any(is.null(mzDeviationInPPM_grouping), length(mzDeviationInPPM_grouping) == 0, nchar(mzDeviationInPPM_grouping) == 0))
error <- TRUE
else{
mzDeviationInPPM_grouping <- as.numeric(mzDeviationInPPM_grouping)
error <- error | is.na(mzDeviationInPPM_grouping)
}
if(doPrecursorDeisotoping){
if(any(is.null(mzDeviationAbsolute_precursorDeisotoping), length(mzDeviationAbsolute_precursorDeisotoping) == 0, nchar(mzDeviationAbsolute_precursorDeisotoping) == 0))
error <- TRUE
else{
mzDeviationAbsolute_precursorDeisotoping <- as.numeric(mzDeviationAbsolute_precursorDeisotoping)
error <- error | is.na(mzDeviationAbsolute_precursorDeisotoping)
}
if(any(is.null(mzDeviationInPPM_precursorDeisotoping), length(mzDeviationInPPM_precursorDeisotoping) == 0, nchar(mzDeviationInPPM_precursorDeisotoping) == 0))
error <- TRUE
else{
mzDeviationInPPM_precursorDeisotoping <- as.numeric(mzDeviationInPPM_precursorDeisotoping)
error <- error | is.na(mzDeviationInPPM_precursorDeisotoping)
}
}
if(any(is.null(maximumRtDifference), length(maximumRtDifference) == 0, nchar(maximumRtDifference) == 0))
error <- TRUE
else{
maximumRtDifference <- as.numeric(maximumRtDifference)
error <- error | is.na(maximumRtDifference)
}
if(doMs2PeakGroupDeisotoping){
if(any(is.null(mzDeviationAbsolute_ms2PeakGroupDeisotoping), length(mzDeviationAbsolute_ms2PeakGroupDeisotoping) == 0, nchar(mzDeviationAbsolute_ms2PeakGroupDeisotoping) == 0))
error <- TRUE
else{
mzDeviationAbsolute_ms2PeakGroupDeisotoping <- as.numeric(mzDeviationAbsolute_ms2PeakGroupDeisotoping)
error <- error | is.na(mzDeviationAbsolute_ms2PeakGroupDeisotoping)
}
if(any(is.null(mzDeviationInPPM_ms2PeakGroupDeisotoping), length(mzDeviationInPPM_ms2PeakGroupDeisotoping) == 0, nchar(mzDeviationInPPM_ms2PeakGroupDeisotoping) == 0))
error <- TRUE
else{
mzDeviationInPPM_ms2PeakGroupDeisotoping <- as.numeric(mzDeviationInPPM_ms2PeakGroupDeisotoping)
error <- error | is.na(mzDeviationInPPM_ms2PeakGroupDeisotoping)
}
}
if(any(is.null(proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere), length(proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere) == 0, nchar(proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere) == 0))
error <- TRUE
else{
proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere <- as.numeric(proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere)
error <- error | is.na(proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere)
}
if(any(is.null(mzDeviationAbsolute_mappingHere), length(mzDeviationAbsolute_mappingHere) == 0, nchar(mzDeviationAbsolute_mappingHere) == 0))
error <- TRUE
else{
mzDeviationAbsolute_mappingHere <- as.numeric(mzDeviationAbsolute_mappingHere)
error <- error | is.na(mzDeviationAbsolute_mappingHere)
}
# if(any(is.null(minimumNumberOfMS2PeaksPerGroupHere), length(minimumNumberOfMS2PeaksPerGroupHere) == 0, nchar(minimumNumberOfMS2PeaksPerGroupHere) == 0))
# error <- TRUE
# else{
# minimumNumberOfMS2PeaksPerGroupHere <- as.numeric(minimumNumberOfMS2PeaksPerGroupHere)
# error <- error | is.na(minimumNumberOfMS2PeaksPerGroupHere)
# }
if(error){
setImportState()
output$fileInfo <- renderText({paste("There are invalid parameter values. Please check the parameters and press 'Import MS\u00B9 and MS/MS data' again.")})
return()
}
## box parameters
print(paste("Observe importMs1Ms2Data", "e", error, "mi", minimumIntensityOfMaximalMS2peak, "mp", minimumProportionOfMS2peaks, "ga", mzDeviationAbsolute_grouping, "gr", mzDeviationInPPM_grouping, "pd", doPrecursorDeisotoping, "pa", mzDeviationAbsolute_precursorDeisotoping, "pr", mzDeviationInPPM_precursorDeisotoping, "mr", maximumRtDifference, "fd", doMs2PeakGroupDeisotoping, "fa", mzDeviationAbsolute_ms2PeakGroupDeisotoping, "fr", mzDeviationInPPM_ms2PeakGroupDeisotoping, "pm", proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere, "ma", mzDeviationAbsolute_mappingHere))
parameterSet <- list()
parameterSet$projectName <- projectName
parameterSet$projectDescription <- projectDescription
parameterSet$toolVersion <- paste(toolName, toolVersion, sep = " ")
parameterSet$minimumIntensityOfMaximalMS2peak <- minimumIntensityOfMaximalMS2peak
parameterSet$minimumProportionOfMS2peaks <- minimumProportionOfMS2peaks
parameterSet$mzDeviationAbsolute_grouping <- mzDeviationAbsolute_grouping
parameterSet$mzDeviationInPPM_grouping <- mzDeviationInPPM_grouping
parameterSet$doPrecursorDeisotoping <- doPrecursorDeisotoping
parameterSet$mzDeviationAbsolute_precursorDeisotoping <- mzDeviationAbsolute_precursorDeisotoping
parameterSet$mzDeviationInPPM_precursorDeisotoping <- mzDeviationInPPM_precursorDeisotoping
parameterSet$maximumRtDifference <- maximumRtDifference
parameterSet$doMs2PeakGroupDeisotoping <- doMs2PeakGroupDeisotoping
parameterSet$mzDeviationAbsolute_ms2PeakGroupDeisotoping <- mzDeviationAbsolute_ms2PeakGroupDeisotoping
parameterSet$mzDeviationInPPM_ms2PeakGroupDeisotoping <- mzDeviationInPPM_ms2PeakGroupDeisotoping
parameterSet$proportionOfMatchingPeaks_ms2PeakGroupDeisotoping <- proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere
parameterSet$mzDeviationAbsolute_mapping <- mzDeviationAbsolute_mappingHere
#parameterSet$minimumNumberOfMS2PeaksPerGroup <- minimumNumberOfMS2PeaksPerGroupHere
parameterSet$neutralLossesPrecursorToFragments <- neutralLossesPrecursorToFragments
parameterSet$neutralLossesFragmentsToFragments <- neutralLossesFragmentsToFragments
#################################################
## convert to project file
## built matrix
error <- NULL
withProgress(message = 'Generating matrix...', value = 0, {
resultObj <- tryCatch(
{
convertToProjectFile(
filePeakMatrix = fileMs1Path,
fileSpectra = fileMs2Path,
parameterSet = parameterSet,
progress = TRUE
)
}, error = function(e) {
error <<- e
}
)
})
if(!is.null(error)){
msg <- paste(
"There occurred an error while processing the input file. Please check the file format and content and try again.", "\n",
"Occurred error: ", error, sep = ""
)
output$fileInfo <- renderText({msg})
showErrorDialog(msg)
setImportState()
return()
}
if(length(resultObj) == 1){
if(resultObj == "Number of spectra is zero"){
msg <- paste("There are no MS/MS spectra which fulfill the given criteria. Please refine parameter 'Spectrum intensity' and try 'Import MS\u00B9 and MS/MS data' again.")
output$fileInfo <- renderText({msg})
showErrorDialog(msg)
setImportState()
return()
}
}
error <- NULL
withProgress(message = 'Processing matrix...', value = 0, {
lines <- sparseMatrixToString(matrixRows = resultObj$matrixRows, matrixCols = resultObj$matrixCols, matrixVals = resultObj$matrixVals, parameterSet = parameterSet)
#################################################
## process project file
dataList <<- tryCatch({
readProjectData(fileLines = lines, progress = TRUE)
}, error = function(e) {
error <<- e
}
)
})
if(!is.null(error)){
msg <- paste(
"There occurred an error while processing the input file. Please check the file format and content and try again.", "\n",
"Occurred error: ", error, sep = ""
)
output$fileInfo <- renderText({msg})
showErrorDialog(msg)
setImportState()
return()
}
print(paste("readProjectData do data finished", dataList$minimumMass))
spectraImport <- paste(
## spectra
resultObj$numberOfParsedSpectra, " / ", resultObj$numberOfSpectraOriginal, " spectra were imported successfully.",
ifelse(test = resultObj$numberOfParsedSpectra < resultObj$numberOfSpectraOriginal, yes = paste(" (",paste( Filter(nchar, c(
ifelse(test = resultObj$numberOfSpectraDiscardedDueToNoPeaks > 0, yes = paste(resultObj$numberOfSpectraDiscardedDueToNoPeaks, " empty", sep = ""), no = ""),
ifelse(test = resultObj$numberOfSpectraDiscardedDueToMaxIntensity > 0, yes = paste(resultObj$numberOfSpectraDiscardedDueToMaxIntensity, " low intensity", sep = ""), no = ""),
ifelse(test = resultObj$numberOfSpectraDiscardedDueToTooHeavy > 0, yes = paste(resultObj$numberOfSpectraDiscardedDueToTooHeavy, " too heavy", sep = ""), no = "")
)), collapse = ", "), ")", sep = ""), no = ""),
sep = ""
)
spectraMapping <- paste(
## mapping
resultObj$numberOfPrecursors, " / ", resultObj$numberOfParsedSpectra, " spectra were successfully mapped to MS\u00B9 features.",
ifelse(test = resultObj$numberOfPrecursors < resultObj$numberOfParsedSpectra, yes = paste(" (",paste( Filter(nchar, c(
#ifelse(test = resultObj$numberOfUnmappedPrecursorsMz > 0, yes = paste(resultObj$numberOfUnmappedPrecursorsMz, " with m/z deviation", sep = ""), no = ""),
#ifelse(test = resultObj$numberOfUnmappedPrecursorsRt > 0, yes = paste(resultObj$numberOfUnmappedPrecursorsRt, " with RT deviation", sep = ""), no = "")
ifelse(test = resultObj$numberOfUnmappedSpectra > 0, yes = paste(resultObj$numberOfUnmappedSpectra, " unmapped", sep = ""), no = "")
)), collapse = ", "), ")", sep = ""), no = ""),
sep = ""
)
fragmentImport <- paste(
## fragments
resultObj$numberOfMS2PeaksAboveThreshold, " / ", resultObj$numberOfMS2PeaksOriginal, " fragments were successfully imported.",
ifelse(test = resultObj$numberOfMS2PeaksAboveThreshold < resultObj$numberOfMS2PeaksOriginal, yes = paste(" (",paste( Filter(nchar, c(
ifelse(test = resultObj$numberOfTooHeavyFragments > 0, yes = paste(resultObj$numberOfTooHeavyFragments, " too heavy", sep = ""), no = ""),
ifelse(test = resultObj$numberOfMS2PeaksBelowThreshold > 0, yes = paste(resultObj$numberOfMS2PeaksBelowThreshold, " low intensity", sep = ""), no = "")
)), collapse = ", "), ")", sep = ""), no = ""),
sep = ""
)
featureImport <- paste(
## MS1 features
resultObj$numberOfPrecursors, " / ", resultObj$numberOfParsedMs1Features, " MS\u00B9 features were successfully imported.",
ifelse(test = resultObj$numberOfPrecursors < resultObj$numberOfParsedMs1Features, yes = paste(" (",paste( Filter(nchar, c(
ifelse(test = resultObj$numberOfRemovedPrecursorIsotopePeaks > 0, yes = paste(resultObj$numberOfRemovedPrecursorIsotopePeaks, " were isotopes", sep = ""), no = ""),
ifelse(test = resultObj$numberOfUnmappedPrecursors > 0, yes = paste(resultObj$numberOfUnmappedPrecursors, " without spectra", sep = ""), no = ""),
ifelse(test = resultObj$numberOfDuplicatedPrecursors > 0, yes = paste(resultObj$numberOfDuplicatedPrecursors, " duplicated", sep = ""), no = "")
)), collapse = ", "), ")", sep = ""), no = ""),
sep = ""
)
msg <- paste(
"The data import was successful.", "<br>",
"<br>",
spectraImport, "<br>",
ifelse(test = resultObj$numberOfParsedMs1Features!=-1, yes = paste(spectraMapping, "<br>", sep = ""), no = ""),
fragmentImport, "<br>",
ifelse(test = resultObj$numberOfParsedMs1Features!=-1, yes = featureImport, no = ""),
sep = ""
)
showInfoDialog(msg)
## MS2
# + returnObj$numberOfSpectraOriginal
# + returnObj$numberOfMS2PeaksOriginal
# - returnObj$numberOfMS2PeaksWithNeutralLosses
# + returnObj$numberOfMS2PeaksAboveThreshold
# + returnObj$numberOfMS2PeaksBelowThreshold
# + returnObj$numberOfTooHeavyFragments
# + returnObj$numberOfSpectraDiscardedDueToNoPeaks
# + returnObj$numberOfSpectraDiscardedDueToMaxIntensity
# + returnObj$numberOfSpectraDiscardedDueToTooHeavy
#
## MS1
# + returnObj$numberOfPrecursors
#
# + returnObj$numberOfDuplicatedPrecursors
# + returnObj$numberOfUnmappedPrecursors
# + returnObj$numberOfUnmappedPrecursorsMz
# + returnObj$numberOfUnmappedPrecursorsRt
# + returnObj$numberOfParsedSpectra
# + returnObj$numberOfParsedMs1Features
# + returnObj$numberOfRemovedPrecursorIsotopePeaks
resetWorkspace()
if(importMS1andMS2data)
state_tabInput$importedOrLoadedFile_s_ <<- c(fileMs1Name, fileMs2Name)
else
state_tabInput$importedOrLoadedFile_s_ <<- c(fileMs2Name)
updateFileInputInfo()
setImportState()
}
obsFileInputSelection <- observeEvent(input$fileInputSelection, {
updateFileInputInfo()
})
obsApplyImportParameterFile <- observeEvent(input$importParameterFileInput$datapath, {
filePath <- input$importParameterFileInput$datapath
fileName <- input$importParameterFileInput$name
print(paste("Observe importParameterFile", fileName))
if(is.null(filePath))
return()
## read and parse
fileContent <- readLines(con = filePath)
parameterSet <- deserializeParameterSetFile(fileContent)
## apply
#projectName2 <- parameterSet$projectName
#projectName2 <- paste(projectName2, " adopted", sep = "")
#updateTextInput (session = session, inputId = "projectName", value = projectName2)
#parameterSet$toolVersion
updateTextInput (session = session, inputId = "minimumIntensityOfMaximalMS2peak", value = parameterSet$minimumIntensityOfMaximalMS2peak)
updateTextInput (session = session, inputId = "minimumProportionOfMS2peaks", value = parameterSet$minimumProportionOfMS2peaks)
updateTextInput (session = session, inputId = "mzDeviationAbsolute_grouping", value = parameterSet$mzDeviationAbsolute_grouping)
updateTextInput (session = session, inputId = "mzDeviationInPPM_grouping", value = parameterSet$mzDeviationInPPM_grouping)
updateCheckboxInput(session = session, inputId = "doPrecursorDeisotoping", value = parameterSet$doPrecursorDeisotoping)
updateTextInput (session = session, inputId = "mzDeviationAbsolute_precursorDeisotoping", value = parameterSet$mzDeviationAbsolute_precursorDeisotoping)
updateTextInput (session = session, inputId = "mzDeviationInPPM_precursorDeisotoping", value = parameterSet$mzDeviationInPPM_precursorDeisotoping)
updateTextInput (session = session, inputId = "maximumRtDifference", value = parameterSet$maximumRtDifference)
updateCheckboxInput(session = session, inputId = "doMs2PeakGroupDeisotoping", value = parameterSet$doMs2PeakGroupDeisotoping)
updateTextInput (session = session, inputId = "mzDeviationAbsolute_ms2PeakGroupDeisotoping", value = parameterSet$mzDeviationAbsolute_ms2PeakGroupDeisotoping)
updateTextInput (session = session, inputId = "mzDeviationInPPM_ms2PeakGroupDeisotoping", value = parameterSet$mzDeviationInPPM_ms2PeakGroupDeisotoping)
#parameterSet$proportionOfMatchingPeaks_ms2PeakGroupDeisotoping
#parameterSet$mzDeviationAbsolute_mapping
#parameterSet$minimumNumberOfMS2PeaksPerGroup
updateCheckboxInput(session = session, inputId = "neutralLossesPrecursorToFragments", value = parameterSet$neutralLossesPrecursorToFragments)
updateCheckboxInput(session = session, inputId = "neutralLossesFragmentsToFragments", value = parameterSet$neutralLossesFragmentsToFragments)
})
updateFileInputInfo <- function(){
fileInputSelection <- input$fileInputSelection
filePath <- input$matrixFile$datapath
fileName <- input$matrixFile$name
fileMs1Path <- input$ms1DataFile$datapath
fileMs1Name <- input$ms1DataFile$name
fileMs2Path <- input$ms2DataFile$datapath
fileMs2Name <- input$ms2DataFile$name
#exampleDataSelection <- input$exampleDataSelection
if(all(fileInputSelection == "Example data"))
output$fileInfo <- renderText({paste("Please press 'Load example data' to load the full example data set")})
if(all(fileInputSelection == "Load project", is.null(filePath)))
output$fileInfo <- renderText({paste("Please select a project file and press 'Load project data'")})
if(all(fileInputSelection == "Load project", !is.null(filePath), any(is.null(state_tabInput$importedOrLoadedFile_s_), fileName != state_tabInput$importedOrLoadedFile_s_)))
output$fileInfo <- renderText({paste("Please press 'Load project data'")})
if(all(fileInputSelection == "Load project", !is.null(filePath), !is.null(state_tabInput$importedOrLoadedFile_s_), fileName == state_tabInput$importedOrLoadedFile_s_))
output$fileInfo <- renderText({paste(fileName)})
if(all(fileInputSelection == "Import data", is.null(fileMs1Path), is.null(fileMs2Path)))
output$fileInfo <- renderText({paste("Please select a metabolite profile and a MS/MS library and press 'Import MS1 and MS/MS data' or select a MS/MS library and press 'Import MS/MS data'")})
if(all(fileInputSelection == "Import data", is.null(fileMs1Path), !is.null(fileMs2Path)))
output$fileInfo <- renderText({paste("Please press 'Import MS/MS data' or select a metabolite profile and press 'Import MS1 and MS/MS data'")})
if(all(fileInputSelection == "Import data", !is.null(fileMs1Path), is.null(fileMs2Path)))
output$fileInfo <- renderText({paste("Please select a MS/MS library and press 'Import MS1 and MS/MS data'")})
if(all(fileInputSelection == "Import data", !is.null(fileMs1Path), !is.null(fileMs2Path), any(is.null(state_tabInput$importedOrLoadedFile_s_), c(fileMs1Name,fileMs2Name) != state_tabInput$importedOrLoadedFile_s_)))
output$fileInfo <- renderText({paste("Please press 'Import MS1 and MS/MS data'")})
if(all(fileInputSelection == "Import data", !is.null(fileMs1Path), !is.null(fileMs2Path), !is.null(state_tabInput$importedOrLoadedFile_s_), c(fileMs1Name,fileMs2Name) == state_tabInput$importedOrLoadedFile_s_))
output$fileInfo <- renderText({paste(fileMs1Name, "\n", fileMs2Name, sep = "")})
}
output$fileInfo <- renderText({
print(paste("init output$fileInfo"))
paste("Please select a project file and press 'Load project data'")
})
suspendOnExitFunctions <- c(suspendOnExitFunctions, function(){
print("Suspending tabInput observers")
obsFile$suspend()
obsLoadProjectData$suspend()
obsLoadExampleData$suspend()
obsImportMs1DataFile$suspend()
obsImportMs2DataFile$suspend()
obsImportMs1Ms2Data$suspend()
obsImportMs2Data$suspend()
obsFileInputSelection$suspend()
obsApplyImportParameterFile$suspend()
})
ipb-halle/MetFamily documentation built on May 11, 2024, 1:09 a.m.
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## data import: fixed parameters
proportionOfMatchingPeaks_ms2PeakGroupDeisotoping <- 0.9
mzDeviationAbsolute_mapping <- 0.01
#minimumNumberOfMS2PeaksPerGroup <- 1
## data
dataList <- NULL
state_tabInput <- reactiveValues(
importedOrLoadedFile_s_ = NULL
)
resetWorkspaceFunctions <- c(resetWorkspaceFunctions, function(){
print("Reset tabInput state")
state_tabInput$importedOrLoadedFile_s_ <<- NULL
})
enableLoadButtons <- function(){
#session$sendCustomMessage("enableButton", "loadProjectData")
#session$sendCustomMessage("enableButton", "loadExampleData")
#session$sendCustomMessage("enableButton", "importMs1Ms2Data")
#session$sendCustomMessage("enableButton", "importMs2Data")
shinyjs::enable("loadProjectData")
shinyjs::enable("loadExampleData")
shinyjs::enable("importMs1Ms2Data")
shinyjs::enable("importMs2Data")
}
disableLoadButtons <- function(){
session$sendCustomMessage("disableButton", "loadProjectData")
session$sendCustomMessage("disableButton", "loadExampleData")
session$sendCustomMessage("disableButton", "importMs1Ms2Data")
session$sendCustomMessage("disableButton", "importMs2Data")
shinyjs::disable("loadProjectData")
shinyjs::disable("loadExampleData")
shinyjs::disable("importMs1Ms2Data")
shinyjs::disable("importMs2Data")
}
obsFile <- observeEvent(input$matrixFile$datapath, {
filePath <- input$matrixFile$datapath
fileName <- input$matrixFile$name
print(paste("Observe file for data", fileName))
if(!is.null(filePath))
shinyjs::enable("loadProjectData")
updateFileInputInfo()
})
obsLoadProjectData <- observeEvent(input$loadProjectData, {
disableLoadButtons()
loadProjectData <- as.numeric(input$loadProjectData)
print(paste("Observe loadProjectData", loadProjectData))
#################################################
## check if button was hit
#if(loadProjectData == loadProjectDataButtonValue)
# return()
#loadProjectDataButtonValue <<- loadProjectData
#################################################
## files
filePath <- input$matrixFile$datapath
loadProjectFile(filePath = filePath)
enableLoadButtons()
})
obsLoadExampleData <- observeEvent(input$loadExampleData, {
disableLoadButtons()
loadExampleData <- as.numeric(input$loadExampleData)
print(paste("Observe loadExampleData", loadExampleData))
#################################################
## check if button was hit
#if(loadExampleData == loadExampleDataButtonValue)
# return()
#loadExampleDataButtonValue <<- loadExampleData
#################################################
## files
filePath <- system.file("extdata/showcase/Project_file_showcase_annotated.csv.gz", package = "MetFamily")
loadProjectFile(filePath = filePath)
enableLoadButtons()
})
loadProjectFile <- function(filePath){
fileName <- basename(filePath)
#########################################################################################
## read data
error <<- NULL
withProgress(message = 'Reading file...', value = 0, {
dataList <<- tryCatch(
{
readClusterDataFromProjectFile(file = filePath, progress = TRUE)
},
error = function(e) {
print(e)
error <<- e
}
)
})
if(!is.null(error)){
print(paste("readClusterDataFromProjectFile resulted in error:", error))
msg <- paste("An error occurred while reading the input files. Please check the file format and content and try again. The error was", error)
output$fileInfo <- renderText({msg})
#session$sendCustomMessage("enableButton", buttonId)
#shinyBS::addPopover(session = session, id = "fileInputSelection", title = "Error", content = "huhu")
msg <- paste(
"An error occurred while reading the input files.",
"Please check the file format and content and try again.",
"The error was:",
"<br>",
error
)
showErrorDialog(msg)
return()
}
print(paste("readClusterDataFromProjectFile finished", dataList$minimumMass))
resetWorkspace()
state_tabInput$importedOrLoadedFile_s_ <<- fileName
updateFileInputInfo()
}
obsImportMs1DataFile <- observeEvent(input$ms1DataFile$datapath, {
fileMs1Path <- input$ms1DataFile$datapath
fileMs1Name <- input$ms1DataFile$name
fileMs2Path <- input$ms2DataFile$datapath
fileMs2Name <- input$ms2DataFile$name
print(paste("Observe import MS1 file", fileMs1Name))
if(all(!is.null(fileMs1Path), !is.null(fileMs2Path)))
shinyjs::enable("importMs1Ms2Data")
else
shinyjs::disable("importMs1Ms2Data")
updateFileInputInfo()
})
obsImportMs2DataFile <- observeEvent(input$ms2DataFile$datapath, {
setImportState()
})
setImportState <- function(){
fileMs1Path <- input$ms1DataFile$datapath
fileMs1Name <- input$ms1DataFile$name
fileMs2Path <- input$ms2DataFile$datapath
fileMs2Name <- input$ms2DataFile$name
print(paste("Observe import MS2 file", fileMs2Name))
if(all(!is.null(fileMs1Path), !is.null(fileMs2Path)))
shinyjs::enable("importMs1Ms2Data")
else
shinyjs::disable("importMs1Ms2Data")
if(!is.null(fileMs2Path))
shinyjs::enable("importMs2Data")
else
shinyjs::disable("importMs2Data")
updateFileInputInfo()
}
obsImportMs1Ms2Data <- observeEvent(input$importMs1Ms2Data, {
disableLoadButtons()
importMs1Ms2Data <- as.numeric(input$importMs1Ms2Data)
print(paste("Observe importMs1Ms2Data", importMs1Ms2Data))
#################################################
## check if button was hit
#if(importMs1Ms2Data == importMs1Ms2DataButtonValue)
# return()
#importMs1Ms2DataButtonValue <<- importMs1Ms2Data
importData(TRUE)
enableLoadButtons()
})
obsImportMs2Data <- observeEvent(input$importMs2Data, {
enableLoadButtons()
importMs2Data <- as.numeric(input$importMs2Data)
print(paste("Observe importMs2Data", importMs2Data))
#################################################
## check if button was hit
#if(importMs2Data == importMs2DataButtonValue)
# return()
#importMs2DataButtonValue <<- importMs2Data
importData(FALSE)
disableLoadButtons()
})
importData <- function(importMS1andMS2data){
#################################################
## files
if(importMS1andMS2data){
fileMs1Path <- input$ms1DataFile$datapath
fileMs1Name <- input$ms1DataFile$name
} else {
fileMs1Path <- NULL
fileMs1Name <- NULL
}
fileMs2Path <- input$ms2DataFile$datapath
fileMs2Name <- input$ms2DataFile$name
#################################################
## params
## project name
projectName <- input$projectName
projectName <- gsub(";", "_", gsub(",", "_", gsub("\t", "_", projectName)))
projectDescription <- input$projectDescription
projectDescription <- gsub(";", "_", gsub(",", "_", gsub("\t", "_", projectDescription)))
## minimum MS2 peak intensity
minimumIntensityOfMaximalMS2peak <- input$minimumIntensityOfMaximalMS2peak
minimumProportionOfMS2peaks <- input$minimumProportionOfMS2peaks
## grouping of MS2 peaks
mzDeviationAbsolute_grouping <- input$mzDeviationAbsolute_grouping
mzDeviationInPPM_grouping <- input$mzDeviationInPPM_grouping
## precursor deisotoping
doPrecursorDeisotoping <- input$doPrecursorDeisotoping
mzDeviationAbsolute_precursorDeisotoping <- input$mzDeviationAbsolute_precursorDeisotoping
mzDeviationInPPM_precursorDeisotoping <- input$mzDeviationInPPM_precursorDeisotoping
maximumRtDifference <- input$maximumRtDifference
## fragment deisotoping
doMs2PeakGroupDeisotoping <- input$doMs2PeakGroupDeisotoping
mzDeviationAbsolute_ms2PeakGroupDeisotoping <- input$mzDeviationAbsolute_ms2PeakGroupDeisotoping
mzDeviationInPPM_ms2PeakGroupDeisotoping <- input$mzDeviationInPPM_ms2PeakGroupDeisotoping
## neutral losses
neutralLossesPrecursorToFragments <- input$neutralLossesPrecursorToFragments
neutralLossesFragmentsToFragments <- input$neutralLossesFragmentsToFragments
#neutralLossesPrecursorToFragments <- TRUE
#neutralLossesFragmentsToFragments <- FALSE
## fixed
proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere <- proportionOfMatchingPeaks_ms2PeakGroupDeisotoping
mzDeviationAbsolute_mappingHere <- mzDeviationAbsolute_mapping
#minimumNumberOfMS2PeaksPerGroupHere <- minimumNumberOfMS2PeaksPerGroup
#################################################
## check params
error <- FALSE
if(any(is.null(minimumIntensityOfMaximalMS2peak), length(minimumIntensityOfMaximalMS2peak) == 0, nchar(minimumIntensityOfMaximalMS2peak) == 0))
error <- TRUE
else{
minimumIntensityOfMaximalMS2peak <- as.numeric(minimumIntensityOfMaximalMS2peak)
error <- error | is.na(minimumIntensityOfMaximalMS2peak)
}
if(any(is.null(minimumProportionOfMS2peaks), length(minimumProportionOfMS2peaks) == 0, nchar(minimumProportionOfMS2peaks) == 0))
error <- TRUE
else{
minimumProportionOfMS2peaks <- as.numeric(minimumProportionOfMS2peaks)
error <- error | is.na(minimumProportionOfMS2peaks)
}
if(any(is.null(mzDeviationAbsolute_grouping), length(mzDeviationAbsolute_grouping) == 0, nchar(mzDeviationAbsolute_grouping) == 0))
error <- TRUE
else{
mzDeviationAbsolute_grouping <- as.numeric(mzDeviationAbsolute_grouping)
error <- error | is.na(mzDeviationAbsolute_grouping)
}
if(any(is.null(mzDeviationInPPM_grouping), length(mzDeviationInPPM_grouping) == 0, nchar(mzDeviationInPPM_grouping) == 0))
error <- TRUE
else{
mzDeviationInPPM_grouping <- as.numeric(mzDeviationInPPM_grouping)
error <- error | is.na(mzDeviationInPPM_grouping)
}
if(doPrecursorDeisotoping){
if(any(is.null(mzDeviationAbsolute_precursorDeisotoping), length(mzDeviationAbsolute_precursorDeisotoping) == 0, nchar(mzDeviationAbsolute_precursorDeisotoping) == 0))
error <- TRUE
else{
mzDeviationAbsolute_precursorDeisotoping <- as.numeric(mzDeviationAbsolute_precursorDeisotoping)
error <- error | is.na(mzDeviationAbsolute_precursorDeisotoping)
}
if(any(is.null(mzDeviationInPPM_precursorDeisotoping), length(mzDeviationInPPM_precursorDeisotoping) == 0, nchar(mzDeviationInPPM_precursorDeisotoping) == 0))
error <- TRUE
else{
mzDeviationInPPM_precursorDeisotoping <- as.numeric(mzDeviationInPPM_precursorDeisotoping)
error <- error | is.na(mzDeviationInPPM_precursorDeisotoping)
}
}
if(any(is.null(maximumRtDifference), length(maximumRtDifference) == 0, nchar(maximumRtDifference) == 0))
error <- TRUE
else{
maximumRtDifference <- as.numeric(maximumRtDifference)
error <- error | is.na(maximumRtDifference)
}
if(doMs2PeakGroupDeisotoping){
if(any(is.null(mzDeviationAbsolute_ms2PeakGroupDeisotoping), length(mzDeviationAbsolute_ms2PeakGroupDeisotoping) == 0, nchar(mzDeviationAbsolute_ms2PeakGroupDeisotoping) == 0))
error <- TRUE
else{
mzDeviationAbsolute_ms2PeakGroupDeisotoping <- as.numeric(mzDeviationAbsolute_ms2PeakGroupDeisotoping)
error <- error | is.na(mzDeviationAbsolute_ms2PeakGroupDeisotoping)
}
if(any(is.null(mzDeviationInPPM_ms2PeakGroupDeisotoping), length(mzDeviationInPPM_ms2PeakGroupDeisotoping) == 0, nchar(mzDeviationInPPM_ms2PeakGroupDeisotoping) == 0))
error <- TRUE
else{
mzDeviationInPPM_ms2PeakGroupDeisotoping <- as.numeric(mzDeviationInPPM_ms2PeakGroupDeisotoping)
error <- error | is.na(mzDeviationInPPM_ms2PeakGroupDeisotoping)
}
}
if(any(is.null(proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere), length(proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere) == 0, nchar(proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere) == 0))
error <- TRUE
else{
proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere <- as.numeric(proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere)
error <- error | is.na(proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere)
}
if(any(is.null(mzDeviationAbsolute_mappingHere), length(mzDeviationAbsolute_mappingHere) == 0, nchar(mzDeviationAbsolute_mappingHere) == 0))
error <- TRUE
else{
mzDeviationAbsolute_mappingHere <- as.numeric(mzDeviationAbsolute_mappingHere)
error <- error | is.na(mzDeviationAbsolute_mappingHere)
}
# if(any(is.null(minimumNumberOfMS2PeaksPerGroupHere), length(minimumNumberOfMS2PeaksPerGroupHere) == 0, nchar(minimumNumberOfMS2PeaksPerGroupHere) == 0))
# error <- TRUE
# else{
# minimumNumberOfMS2PeaksPerGroupHere <- as.numeric(minimumNumberOfMS2PeaksPerGroupHere)
# error <- error | is.na(minimumNumberOfMS2PeaksPerGroupHere)
# }
if(error){
setImportState()
output$fileInfo <- renderText({paste("There are invalid parameter values. Please check the parameters and press 'Import MS\u00B9 and MS/MS data' again.")})
return()
}
## box parameters
print(paste("Observe importMs1Ms2Data", "e", error, "mi", minimumIntensityOfMaximalMS2peak, "mp", minimumProportionOfMS2peaks, "ga", mzDeviationAbsolute_grouping, "gr", mzDeviationInPPM_grouping, "pd", doPrecursorDeisotoping, "pa", mzDeviationAbsolute_precursorDeisotoping, "pr", mzDeviationInPPM_precursorDeisotoping, "mr", maximumRtDifference, "fd", doMs2PeakGroupDeisotoping, "fa", mzDeviationAbsolute_ms2PeakGroupDeisotoping, "fr", mzDeviationInPPM_ms2PeakGroupDeisotoping, "pm", proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere, "ma", mzDeviationAbsolute_mappingHere))
parameterSet <- list()
parameterSet$projectName <- projectName
parameterSet$projectDescription <- projectDescription
parameterSet$toolVersion <- paste(toolName, toolVersion, sep = " ")
parameterSet$minimumIntensityOfMaximalMS2peak <- minimumIntensityOfMaximalMS2peak
parameterSet$minimumProportionOfMS2peaks <- minimumProportionOfMS2peaks
parameterSet$mzDeviationAbsolute_grouping <- mzDeviationAbsolute_grouping
parameterSet$mzDeviationInPPM_grouping <- mzDeviationInPPM_grouping
parameterSet$doPrecursorDeisotoping <- doPrecursorDeisotoping
parameterSet$mzDeviationAbsolute_precursorDeisotoping <- mzDeviationAbsolute_precursorDeisotoping
parameterSet$mzDeviationInPPM_precursorDeisotoping <- mzDeviationInPPM_precursorDeisotoping
parameterSet$maximumRtDifference <- maximumRtDifference
parameterSet$doMs2PeakGroupDeisotoping <- doMs2PeakGroupDeisotoping
parameterSet$mzDeviationAbsolute_ms2PeakGroupDeisotoping <- mzDeviationAbsolute_ms2PeakGroupDeisotoping
parameterSet$mzDeviationInPPM_ms2PeakGroupDeisotoping <- mzDeviationInPPM_ms2PeakGroupDeisotoping
parameterSet$proportionOfMatchingPeaks_ms2PeakGroupDeisotoping <- proportionOfMatchingPeaks_ms2PeakGroupDeisotopingHere
parameterSet$mzDeviationAbsolute_mapping <- mzDeviationAbsolute_mappingHere
#parameterSet$minimumNumberOfMS2PeaksPerGroup <- minimumNumberOfMS2PeaksPerGroupHere
parameterSet$neutralLossesPrecursorToFragments <- neutralLossesPrecursorToFragments
parameterSet$neutralLossesFragmentsToFragments <- neutralLossesFragmentsToFragments
#################################################
## convert to project file
## built matrix
error <- NULL
withProgress(message = 'Generating matrix...', value = 0, {
resultObj <- tryCatch(
{
convertToProjectFile(
filePeakMatrix = fileMs1Path,
fileSpectra = fileMs2Path,
parameterSet = parameterSet,
progress = TRUE
)
}, error = function(e) {
error <<- e
}
)
})
if(!is.null(error)){
msg <- paste(
"There occurred an error while processing the input file. Please check the file format and content and try again.", "\n",
"Occurred error: ", error, sep = ""
)
output$fileInfo <- renderText({msg})
showErrorDialog(msg)
setImportState()
return()
}
if(length(resultObj) == 1){
if(resultObj == "Number of spectra is zero"){
msg <- paste("There are no MS/MS spectra which fulfill the given criteria. Please refine parameter 'Spectrum intensity' and try 'Import MS\u00B9 and MS/MS data' again.")
output$fileInfo <- renderText({msg})
showErrorDialog(msg)
setImportState()
return()
}
}
error <- NULL
withProgress(message = 'Processing matrix...', value = 0, {
lines <- sparseMatrixToString(matrixRows = resultObj$matrixRows, matrixCols = resultObj$matrixCols, matrixVals = resultObj$matrixVals, parameterSet = parameterSet)
#################################################
## process project file
dataList <<- tryCatch({
readProjectData(fileLines = lines, progress = TRUE)
}, error = function(e) {
error <<- e
}
)
})
if(!is.null(error)){
msg <- paste(
"There occurred an error while processing the input file. Please check the file format and content and try again.", "\n",
"Occurred error: ", error, sep = ""
)
output$fileInfo <- renderText({msg})
showErrorDialog(msg)
setImportState()
return()
}
print(paste("readProjectData do data finished", dataList$minimumMass))
spectraImport <- paste(
## spectra
resultObj$numberOfParsedSpectra, " / ", resultObj$numberOfSpectraOriginal, " spectra were imported successfully.",
ifelse(test = resultObj$numberOfParsedSpectra < resultObj$numberOfSpectraOriginal, yes = paste(" (",paste( Filter(nchar, c(
ifelse(test = resultObj$numberOfSpectraDiscardedDueToNoPeaks > 0, yes = paste(resultObj$numberOfSpectraDiscardedDueToNoPeaks, " empty", sep = ""), no = ""),
ifelse(test = resultObj$numberOfSpectraDiscardedDueToMaxIntensity > 0, yes = paste(resultObj$numberOfSpectraDiscardedDueToMaxIntensity, " low intensity", sep = ""), no = ""),
ifelse(test = resultObj$numberOfSpectraDiscardedDueToTooHeavy > 0, yes = paste(resultObj$numberOfSpectraDiscardedDueToTooHeavy, " too heavy", sep = ""), no = "")
)), collapse = ", "), ")", sep = ""), no = ""),
sep = ""
)
spectraMapping <- paste(
## mapping
resultObj$numberOfPrecursors, " / ", resultObj$numberOfParsedSpectra, " spectra were successfully mapped to MS\u00B9 features.",
ifelse(test = resultObj$numberOfPrecursors < resultObj$numberOfParsedSpectra, yes = paste(" (",paste( Filter(nchar, c(
#ifelse(test = resultObj$numberOfUnmappedPrecursorsMz > 0, yes = paste(resultObj$numberOfUnmappedPrecursorsMz, " with m/z deviation", sep = ""), no = ""),
#ifelse(test = resultObj$numberOfUnmappedPrecursorsRt > 0, yes = paste(resultObj$numberOfUnmappedPrecursorsRt, " with RT deviation", sep = ""), no = "")
ifelse(test = resultObj$numberOfUnmappedSpectra > 0, yes = paste(resultObj$numberOfUnmappedSpectra, " unmapped", sep = ""), no = "")
)), collapse = ", "), ")", sep = ""), no = ""),
sep = ""
)
fragmentImport <- paste(
## fragments
resultObj$numberOfMS2PeaksAboveThreshold, " / ", resultObj$numberOfMS2PeaksOriginal, " fragments were successfully imported.",
ifelse(test = resultObj$numberOfMS2PeaksAboveThreshold < resultObj$numberOfMS2PeaksOriginal, yes = paste(" (",paste( Filter(nchar, c(
ifelse(test = resultObj$numberOfTooHeavyFragments > 0, yes = paste(resultObj$numberOfTooHeavyFragments, " too heavy", sep = ""), no = ""),
ifelse(test = resultObj$numberOfMS2PeaksBelowThreshold > 0, yes = paste(resultObj$numberOfMS2PeaksBelowThreshold, " low intensity", sep = ""), no = "")
)), collapse = ", "), ")", sep = ""), no = ""),
sep = ""
)
featureImport <- paste(
## MS1 features
resultObj$numberOfPrecursors, " / ", resultObj$numberOfParsedMs1Features, " MS\u00B9 features were successfully imported.",
ifelse(test = resultObj$numberOfPrecursors < resultObj$numberOfParsedMs1Features, yes = paste(" (",paste( Filter(nchar, c(
ifelse(test = resultObj$numberOfRemovedPrecursorIsotopePeaks > 0, yes = paste(resultObj$numberOfRemovedPrecursorIsotopePeaks, " were isotopes", sep = ""), no = ""),
ifelse(test = resultObj$numberOfUnmappedPrecursors > 0, yes = paste(resultObj$numberOfUnmappedPrecursors, " without spectra", sep = ""), no = ""),
ifelse(test = resultObj$numberOfDuplicatedPrecursors > 0, yes = paste(resultObj$numberOfDuplicatedPrecursors, " duplicated", sep = ""), no = "")
)), collapse = ", "), ")", sep = ""), no = ""),
sep = ""
)
msg <- paste(
"The data import was successful.", "<br>",
"<br>",
spectraImport, "<br>",
ifelse(test = resultObj$numberOfParsedMs1Features!=-1, yes = paste(spectraMapping, "<br>", sep = ""), no = ""),
fragmentImport, "<br>",
ifelse(test = resultObj$numberOfParsedMs1Features!=-1, yes = featureImport, no = ""),
sep = ""
)
showInfoDialog(msg)
## MS2
# + returnObj$numberOfSpectraOriginal
# + returnObj$numberOfMS2PeaksOriginal
# - returnObj$numberOfMS2PeaksWithNeutralLosses
# + returnObj$numberOfMS2PeaksAboveThreshold
# + returnObj$numberOfMS2PeaksBelowThreshold
# + returnObj$numberOfTooHeavyFragments
# + returnObj$numberOfSpectraDiscardedDueToNoPeaks
# + returnObj$numberOfSpectraDiscardedDueToMaxIntensity
# + returnObj$numberOfSpectraDiscardedDueToTooHeavy
#
## MS1
# + returnObj$numberOfPrecursors
#
# + returnObj$numberOfDuplicatedPrecursors
# + returnObj$numberOfUnmappedPrecursors
# + returnObj$numberOfUnmappedPrecursorsMz
# + returnObj$numberOfUnmappedPrecursorsRt
# + returnObj$numberOfParsedSpectra
# + returnObj$numberOfParsedMs1Features
# + returnObj$numberOfRemovedPrecursorIsotopePeaks
resetWorkspace()
if(importMS1andMS2data)
state_tabInput$importedOrLoadedFile_s_ <<- c(fileMs1Name, fileMs2Name)
else
state_tabInput$importedOrLoadedFile_s_ <<- c(fileMs2Name)
updateFileInputInfo()
setImportState()
}
obsFileInputSelection <- observeEvent(input$fileInputSelection, {
updateFileInputInfo()
})
obsApplyImportParameterFile <- observeEvent(input$importParameterFileInput$datapath, {
filePath <- input$importParameterFileInput$datapath
fileName <- input$importParameterFileInput$name
print(paste("Observe importParameterFile", fileName))
if(is.null(filePath))
return()
## read and parse
fileContent <- readLines(con = filePath)
parameterSet <- deserializeParameterSetFile(fileContent)
## apply
#projectName2 <- parameterSet$projectName
#projectName2 <- paste(projectName2, " adopted", sep = "")
#updateTextInput (session = session, inputId = "projectName", value = projectName2)
#parameterSet$toolVersion
updateTextInput (session = session, inputId = "minimumIntensityOfMaximalMS2peak", value = parameterSet$minimumIntensityOfMaximalMS2peak)
updateTextInput (session = session, inputId = "minimumProportionOfMS2peaks", value = parameterSet$minimumProportionOfMS2peaks)
updateTextInput (session = session, inputId = "mzDeviationAbsolute_grouping", value = parameterSet$mzDeviationAbsolute_grouping)
updateTextInput (session = session, inputId = "mzDeviationInPPM_grouping", value = parameterSet$mzDeviationInPPM_grouping)
updateCheckboxInput(session = session, inputId = "doPrecursorDeisotoping", value = parameterSet$doPrecursorDeisotoping)
updateTextInput (session = session, inputId = "mzDeviationAbsolute_precursorDeisotoping", value = parameterSet$mzDeviationAbsolute_precursorDeisotoping)
updateTextInput (session = session, inputId = "mzDeviationInPPM_precursorDeisotoping", value = parameterSet$mzDeviationInPPM_precursorDeisotoping)
updateTextInput (session = session, inputId = "maximumRtDifference", value = parameterSet$maximumRtDifference)
updateCheckboxInput(session = session, inputId = "doMs2PeakGroupDeisotoping", value = parameterSet$doMs2PeakGroupDeisotoping)
updateTextInput (session = session, inputId = "mzDeviationAbsolute_ms2PeakGroupDeisotoping", value = parameterSet$mzDeviationAbsolute_ms2PeakGroupDeisotoping)
updateTextInput (session = session, inputId = "mzDeviationInPPM_ms2PeakGroupDeisotoping", value = parameterSet$mzDeviationInPPM_ms2PeakGroupDeisotoping)
#parameterSet$proportionOfMatchingPeaks_ms2PeakGroupDeisotoping
#parameterSet$mzDeviationAbsolute_mapping
#parameterSet$minimumNumberOfMS2PeaksPerGroup
updateCheckboxInput(session = session, inputId = "neutralLossesPrecursorToFragments", value = parameterSet$neutralLossesPrecursorToFragments)
updateCheckboxInput(session = session, inputId = "neutralLossesFragmentsToFragments", value = parameterSet$neutralLossesFragmentsToFragments)
})
updateFileInputInfo <- function(){
fileInputSelection <- input$fileInputSelection
filePath <- input$matrixFile$datapath
fileName <- input$matrixFile$name
fileMs1Path <- input$ms1DataFile$datapath
fileMs1Name <- input$ms1DataFile$name
fileMs2Path <- input$ms2DataFile$datapath
fileMs2Name <- input$ms2DataFile$name
#exampleDataSelection <- input$exampleDataSelection
if(all(fileInputSelection == "Example data"))
output$fileInfo <- renderText({paste("Please press 'Load example data' to load the full example data set")})
if(all(fileInputSelection == "Load project", is.null(filePath)))
output$fileInfo <- renderText({paste("Please select a project file and press 'Load project data'")})
if(all(fileInputSelection == "Load project", !is.null(filePath), any(is.null(state_tabInput$importedOrLoadedFile_s_), fileName != state_tabInput$importedOrLoadedFile_s_)))
output$fileInfo <- renderText({paste("Please press 'Load project data'")})
if(all(fileInputSelection == "Load project", !is.null(filePath), !is.null(state_tabInput$importedOrLoadedFile_s_), fileName == state_tabInput$importedOrLoadedFile_s_))
output$fileInfo <- renderText({paste(fileName)})
if(all(fileInputSelection == "Import data", is.null(fileMs1Path), is.null(fileMs2Path)))
output$fileInfo <- renderText({paste("Please select a metabolite profile and a MS/MS library and press 'Import MS1 and MS/MS data' or select a MS/MS library and press 'Import MS/MS data'")})
if(all(fileInputSelection == "Import data", is.null(fileMs1Path), !is.null(fileMs2Path)))
output$fileInfo <- renderText({paste("Please press 'Import MS/MS data' or select a metabolite profile and press 'Import MS1 and MS/MS data'")})
if(all(fileInputSelection == "Import data", !is.null(fileMs1Path), is.null(fileMs2Path)))
output$fileInfo <- renderText({paste("Please select a MS/MS library and press 'Import MS1 and MS/MS data'")})
if(all(fileInputSelection == "Import data", !is.null(fileMs1Path), !is.null(fileMs2Path), any(is.null(state_tabInput$importedOrLoadedFile_s_), c(fileMs1Name,fileMs2Name) != state_tabInput$importedOrLoadedFile_s_)))
output$fileInfo <- renderText({paste("Please press 'Import MS1 and MS/MS data'")})
if(all(fileInputSelection == "Import data", !is.null(fileMs1Path), !is.null(fileMs2Path), !is.null(state_tabInput$importedOrLoadedFile_s_), c(fileMs1Name,fileMs2Name) == state_tabInput$importedOrLoadedFile_s_))
output$fileInfo <- renderText({paste(fileMs1Name, "\n", fileMs2Name, sep = "")})
}
output$fileInfo <- renderText({
print(paste("init output$fileInfo"))
paste("Please select a project file and press 'Load project data'")
})
suspendOnExitFunctions <- c(suspendOnExitFunctions, function(){
print("Suspending tabInput observers")
obsFile$suspend()
obsLoadProjectData$suspend()
obsLoadExampleData$suspend()
obsImportMs1DataFile$suspend()
obsImportMs2DataFile$suspend()
obsImportMs1Ms2Data$suspend()
obsImportMs2Data$suspend()
obsFileInputSelection$suspend()
obsApplyImportParameterFile$suspend()
})
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