R/msgfGUI.R
In thomasp85/pepmapsGUI: GUI elements for various parts of pepmaps
# TODO: Add comment
#
# Author: Thomas
###############################################################################
library(pepmaps)
library(RGtk2)
library(ggplot2)
library(scales)
library(plyr)
library(cairoDevice)
library(grid)
library(mzR)
library(XML)
library(Biostrings)
filelist <- rGtkDataFrame(data.frame(Datafiles=character(), stringsAsFactors=FALSE))
gSignalConnect(filelist, 'row-inserted', f=function(treemodel, treepath, treeiter){
validButtons()
})
gSignalConnect(filelist, 'row-deleted', f=function(treemodel, treepath){
validButtons()
})
settingsSetNames <- c('New', 'Placeholder 1', 'Placeholder 2', 'Placeholder 3')
rawResults <- rGtkDataFrame(data.frame(SpecFile=character(), SpecID=character(), ScanNum=numeric(), FragMethod=character(), Precursor=numeric(), IsotopeError=numeric(), PrecursorError=numeric(), Charge=numeric(), Peptide=character(), Protein=character(), DeNovoScore=numeric(), MSGFScore=numeric(), SpecEValue=numeric(), EValue=numeric(), QValue=numeric(), PepQValue=numeric(), realPeptide=character(), '.vis'=logical(), stringsAsFactors=FALSE, check.names=FALSE))
#gSignalConnect(rawResults, 'row-inserted', f=function(treemodel, ...){
# resultBox$setSensitive(TRUE)
# peptides$setFrame(data.frame(Peptides=unique(rawResults[which(rawResults[,'.vis']), 'realPeptide'], stringsAsFactors=FALSE)))
# proteins$setFrame(data.frame(Proteins=unique(rawResults[which(rawResults[,'.vis']), 'Protein'], stringsAsFactors=FALSE)))
# })
#gSignalConnect(rawResults, 'row-deleted', f=function(treemodel, ...){
# if(nrow(rawResults[]) == 0){
# nPepID$setText('')
# nProtID$setText('')
# protIntersect$setText('')
# charge$setText(paste('', '\t(min)\n', '', '\t(median)\n', '', '\t(max)', sep=''))
# dev.set(FDRplot$getData('Device'))
# grid.newpage()
# dev.set(spectrumPlot$getData('Device'))
# grid.newpage()
# resultBox$setSensitive(FALSE)
# } else {
# peptides$setFrame(data.frame(Peptides=unique(rawResults[which(rawResults[,'.vis']), 'realPeptide'], stringsAsFactors=FALSE)))
# proteins$setFrame(data.frame(Proteins=unique(rawResults[which(rawResults[,'.vis']), 'Protein'], stringsAsFactors=FALSE)))
# sampleSelect$setActive(0)
# plotFDR(model=rawResults, sample='All', device=FDRplot$getData('Device'))
# }
# })
rawResultsFilter <- rawResults$filter()
rawResultsFilter$setVisibleColumn(ncol(rawResults)-1)
samples <- rGtkDataFrame(data.frame(Samples='All', '.notAll'=FALSE, loaded=FALSE, database=NA, rawfile=NA, resultfile=NA, check.names=FALSE, stringsAsFactors=FALSE))
gSignalConnect(samples, 'row-inserted', f=function(treemodel, treepath, treeiter, user.data){
nPepID$setText(length(peptides[]))
nProtID$setText(length(proteins[]))
protIntersect$setText(calcProtIntersect())
chargeSum <- summary(rawResults[rawResults[,'.vis'], 'Charge'])
charge$setText(paste(chargeSum['Min.'], '\t(min)\n', chargeSum['Median'], '\t(median)\n', chargeSum['Max.'], '\t(max)', sep=''))
})
samplesFilter <- samples$filter()
samplesFilter$setVisibleColumn(1)
peptides <- rGtkDataFrame(data.frame(Peptides=character(), stringsAsFactors=FALSE))
proteins <- rGtkDataFrame(data.frame(Proteins=character(), stringsAsFactors=FALSE))
tempPeptideList <- rGtkDataFrame(data.frame(Peptides=character(), stringsAsFactors=FALSE))
tempSampleList <- rGtkDataFrame(data.frame(Samples=character(), stringsAsFactors=FALSE))
collectSettings <- function(){
ans <- list()
ans$tolerance <- paste(sub(',', '.', toleranceValue$getText()), toleranceUnit$getActiveText(), sep='')
ans$isotopeError <- c(isotopeErrorLow$getValue(), isotopeErrorHigh$getValue())
ans$tda <- tdaToggle$getMode()
ans$fragmentation <- fragmentation$getActiveText()
ans$instrument <- instrument$getActiveText()
ans$protease <- enzyme$getActiveText()
ans$termini <- termini$getValue()
if(modification$getText() != 'Modification file...' & modification$getText() != ''){
if(file.exists(modification$getText())){
ans$modification <- modification$getText()
} else {
modificationWarning <- gtkMessageDialog(parent=mainWindow, flags='modal', type='warnings', buttons='ok', 'Modification file ignored', show=FALSE)
modificationWarning['title'] <- 'File problem'
gSignalConnect(modificationWarning, 'response', f=function(dialog, response, data){
dialog$destroy()
})
modificationWarning$show()
}
} else {}
ans$lengthRange <- c(lengthLow$getValue(), lengthHigh$getValue())
ans$chargeRange <- c(chargeLow$getValue(), chargeHigh$getValue())
ans$matches <- match$getValue()
ans
}
validButtons <- function(){
fileCheck <- nrow(filelist[drop=FALSE]) == 0
databaseCheck <- database$getText() == 'Database fasta file...' | database$getText() == ''
if(!databaseCheck){
databaseCheck <- !file.exists(database$getText())
} else {}
modificationCheck <- modification$getText() == 'Modification file...' | modification$getText() == ''
if(!modificationCheck){
modificationCheck <- !file.exists(modification$getText())
} else {
modificationCheck <- FALSE
}
if(fileCheck){
fileRemoveButton['sensitive'] <- FALSE
} else {
fileRemoveButton['sensitive'] <- TRUE
}
if(any(c(fileCheck, databaseCheck, modificationCheck))){
analyzeButton['sensitive'] <- FALSE
} else {
analyzeButton['sensitive'] <- TRUE
}
}
rawFilter <- function(data, sample, FDR, decoy=TRUE){
if(decoy){
ifelse(data[,1] == sample | sample == 'All', ifelse(data[,15] <= FDR, ifelse(!grepl('XXX_', data[,10]), TRUE, FALSE), FALSE), FALSE)
} else {
ifelse(data[,1] == sample | sample == 'All', ifelse(data[,15] <= FDR, TRUE, FALSE), FALSE)
}
}
sampleFilter <- function(){
ans <- sampleSelect$getActiveIter()
if(ans$retval){
ans <- samples$getValue(ans$iter, 0)$value
} else {
ans <- 'All'
}
ans
}
rawUpdated <- function(){
if(nrow(rawResults[]) == 0){
resultNotebook$setCurrentPage(resultNotebook$pageNum(summaryTab))
nPepID$setText('')
nProtID$setText('')
protIntersect$setText('')
charge$setText(paste('', '\t(min)\n', '', '\t(median)\n', '', '\t(max)', sep=''))
peptides$setFrame(data.frame(Peptides=character(), stringsAsFactors=FALSE))
proteins$setFrame(data.frame(Proteins=character(), stringsAsFactors=FALSE))
tempPeptideList$setFrame(data.frame(Peptides=character(), stringsAsFactors=FALSE))
tempSampleList$setFrame(data.frame(Samples=character(), stringsAsFactors=FALSE))
dev.set(FDRplot$getData('Device'))
grid.newpage()
dev.set(spectrumPlot$getData('Device'))
grid.newpage()
resultBox$setSensitive(FALSE)
} else {
resultBox$setSensitive(TRUE)
peptides$setFrame(data.frame(Peptides=unique(rawResults[which(rawResults[,'.vis']), 'realPeptide'], stringsAsFactors=FALSE)))
proteins$setFrame(data.frame(Proteins=unique(rawResults[which(rawResults[,'.vis']), 'Protein'], stringsAsFactors=FALSE)))
sampleSelect$setActive(0)
plotFDR(model=rawResults, sample='All', device=FDRplot$getData('Device'))
}
}
filterUpdated <- function(FDRChange=TRUE, SampleChange=TRUE){
if(length(samples[, 'Samples']) > 1){
rawResults[,'.vis'] <- rawFilter(rawResults[], sample=sampleFilter(), FDR=FDR$getValue())
peptides$setFrame(data.frame(Peptides=unique(rawResults[which(rawResults[,'.vis']), 'realPeptide'], stringsAsFactors=FALSE)))
proteins$setFrame(data.frame(Proteins=unique(rawResults[which(rawResults[,'.vis']), 'Protein'], stringsAsFactors=FALSE)))
#plotPepNumber(rawResults, sampleFilter(), FDR$getValue(), pepNumberPlot$getData('Device'))
nPepID$setText(length(peptides[]))
nProtID$setText(length(proteins[]))
chargeSum <- summary(rawResults[rawResults[,'.vis'], 'Charge'])
charge$setText(paste(chargeSum['Min.'], '\t(min)\n', chargeSum['Median'], '\t(median)\n', chargeSum['Max.'], '\t(max)', sep=''))
if(SampleChange){
plotFDR(rawResults, sampleFilter(), device=FDRplot$getData('Device'))
} else {}
if(FDRChange){
#FDR specific actions here
} else {}
} else {}
}
plotFDR <- function(model, sample, device){
if(sample == 'All'){
df <- model[]
} else {
df <- model[model[,'SpecFile'] == sample, ]
}
df$Score <- -log(df$SpecEValue)
df$decoy <- grepl('XXX_', df$Protein)
p <- ggplot(data=df, aes(x=Score, group=decoy, fill=decoy)) + theme_bw()
p <- p + geom_density(alpha=I(0.5)) + scale_fill_manual('', breaks=c(FALSE, TRUE), labels=c('Database ', 'Decoy'), values=c('#468966', '#B64926'))
p <- p + scale_x_continuous(limits=c(0, max(df$Score)), expand=c(0,0)) + scale_y_continuous(expand=c(0,0))
p <- p + theme(panel.border=element_blank(), panel.grid=element_blank(), axis.line=element_line(size=0.5), legend.position='bottom')
dev.set(device)
print(p)
}
plotPepNumber <- function(model, sample, FDR, device){
if(sample == 'All'){
df <- model[model[,'QValue'] <= FDR,]
} else {
df <- model[model[,'SpecFile'] == sample & model[,'QValue'] <= FDR, ]
}
df <- df[!grepl('XXX_', df$Protein),]
nPep <- daply(df, .(Protein), function(x) length(unique(x$realPeptide)))
p <- ggplot(data=data.frame(nPep=nPep)) + geom_histogram(aes(x=nPep)) + coord_flip() + scale_x_reverse()
p <- p + theme_bw() + theme(panel.border=element_blank(), panel.grid=element_blank(), axis.line=element_line(size=0.5))
dev.set(device)
print(p)
}
calcProtIntersect <- function(){
df <- rawResults[]
df <- df[!grepl('XXX_', df$Protein),]
df <- df[df$QValue <= FDR$getValue(), ]
names(df)[1] <- sub('#', '', names(df)[1])
df <- dlply(df, .(SpecFile), function(x) unique(x$Protein))
length(Reduce(intersect, df))
}
traceIon <- function(data, index, mz, ppm){
indexRange <- c(1, length(data))
mzWin <- c(mz-(mz/1000000)*ppm, mz+(mz/1000000)*ppm)
scan <- peaks(data, index)
mzIndex <- which(scan[,1] > mzWin[1] & scan[,1] < mzWin[2])
if(length(mzIndex) == 0){
intensity <- c()
retention <- c()
} else {
if(length(mzIndex) != 1){
mzIndex <- mzIndex[which.max(scan[mzIndex, 2])]
} else {}
intensity <- c(scan[mzIndex, 2])
retention <- c(header(data, index)$retentionTime)
}
indexBack <- index
indexForward <- index
doBreak <- FALSE
nextIter <- 1
while(as.logical(nextIter)){
indexBack <- indexBack-1
while(header(data, indexBack)$msLevel == 2){
indexBack <- indexBack-1
if(indexBack <= indexRange[1]){
doBreak <- TRUE
break
}
}
if(doBreak) break
if(indexBack < 1) break
scan <- peaks(data, indexBack)
mzIndex <- which(scan[,1] > mzWin[1] & scan[,1] < mzWin[2])
if(length(mzIndex) == 0){
nextIter <- nextIter + 1
} else {
if(length(mzIndex) != 1){
mzIndex <- mzIndex[which.max(scan[mzIndex, 2])]
} else {}
intensity <- c(scan[mzIndex, 2], intensity)
retention <- c(header(data, indexBack)$retentionTime, retention)
}
if(nextIter > 2){
nextIter <- 0
}
if(indexBack <= indexRange[1]){
nextIter <- 0
}
}
nextIter <- 1
doBreak <- FALSE
while(as.logical(nextIter)){
indexForward <- indexForward+1
while(header(data, indexForward)$msLevel == 2){
indexForward <- indexForward+1
if(indexForward >= indexRange[2]){
doBreak <- TRUE
break
}
}
if(doBreak) break
scan <- peaks(data, indexForward)
mzIndex <- which(scan[,1] > mzWin[1] & scan[,1] < mzWin[2])
if(length(mzIndex) == 0){
nextIter <- nextIter + 1
} else {
if(length(mzIndex) != 1){
mzIndex <- mzIndex[which.max(scan[mzIndex, 2])]
} else {}
intensity <- c(intensity, scan[mzIndex, 2])
retention <- c(retention, header(data, indexForward)$retentionTime)
}
if(nextIter > 2){
nextIter <- 0
}
if(indexForward >= indexRange[2]){
nextIter <- 0
}
}
data.frame(intensity, retention)
}
plotSpectrum <- function(data, scan, seq, ppm=40, device, ionTrace=TRUE, ions='aby', neutralLosses=TRUE){
if(missing(device)){
device <- dev.cur()
}
index <- which(header(data)$acquisitionNum == scan)
scanInfo <- header(data, index)
spec <- peaks(data, index)
spec <- data.frame(mz=spec[,1], intensity=spec[,2], ymin=0)
if(scanInfo$msLevel > 1){
precursor <- which.min(abs(spec$mz-scanInfo$precursorMZ))
if(abs(spec$mz[precursor]-scanInfo$precursorMZ) < (scanInfo$precursorMZ/1000000)*ppm){
precursor <- spec[precursor, , drop=FALSE]
} else {
precursor <- data.frame()
}
} else {
precursor <- data.frame()
}
if(!missing(seq)){
p <- ggplot() + geom_linerange(data=spec, aes(x=mz, ymax=intensity, ymin=ymin), colour=I('grey'))
if(nrow(precursor) != 0){
p <- p + geom_point(data=precursor, aes(x=mz, y=intensity), size=I(3), colour=I('#B64926'))
}
ionlab <- data.frame(spec, ion=NA)
ionlist <- pepmaps:::fragPattern(seq, ions=ions, neutralLosses=neutralLosses)
for(i in 1:nrow(ionlist)){
ind <- which(ionlab$mz < ionlist$mz[i]+(ionlist$mz[i]/1000000)*ppm & ionlab$mz > ionlist$mz[i]-(ionlist$mz[i]/1000000)*ppm)
if(length(ind) == 1){
ionlab$ion[ind] <- ionlist$ion[i]
} else if(length(ind) > 1){
ind <- ind[which.min(abs(ionlab$mz[ind]-ionlist$mz[i]))]
ionlab$ion[ind] <- ionlist$ion[i]
} else {}
}
ionlab <- ionlab[!is.na(ionlab$ion),]
if(nrow(ionlab) != 0){
p <- p + geom_linerange(data=ionlab, aes(x=mz, ymax=intensity, ymin=ymin))
p <- p + geom_text(data=ionlab, aes(x=mz, y=intensity, label=ion), colour=I('#468966'), vjust=-0.5, size=4)
} else {}
} else {}
p <- p + theme_bw() + theme(panel.border=element_blank(), panel.grid=element_blank(), axis.line=element_line(size=0.5), legend.position='bottom')
p <- p + scale_y_continuous('Intensity', expand=c(0,0), limits=c(0, max(spec$intensity)*1.1))
if(ionTrace){
parentIndex <- which(header(data)$acquisitionNum == scanInfo$precursorScanNum)
parentInfo <- header(data, parentIndex)
intensity <- peaks(data, parentIndex)
parentData <- data.frame(retention=parentInfo$retentionTime, intensity=intensity[which.min(abs(intensity[, 1]-scanInfo$precursorMZ)), 2])
trace <- traceIon(data, parentIndex, scanInfo$precursorMZ, ppm)
parentLines <- data.frame(x=c(min(trace$retention), parentData$retention), xend=c(parentData$retention, parentData$retention), y=c(parentData$intensity, min(trace$intensity)), yend=c(parentData$intensity, parentData$intensity))
q <- ggplot(data=trace, aes(x=retention, y=intensity)) + geom_line()
q <- q + geom_segment(data=parentLines, aes(x=x, xend=xend, y=y, yend=yend), linetype=I(2))
q <- q + geom_point(data=parentData, size=I(3), colour=I('#B64926'))
q <- q + theme_minimal() + theme(panel.grid=element_blank(), axis.ticks=element_blank(), plot.background=element_rect(colour=alpha('#F5F5F5', 0.75), fill=alpha('#F5F5F5', 0.75)), plot.margin=unit(c(10, 10, 0, 0), 'points'))
q <- q + scale_y_continuous('', expand=c(0,0), breaks=parentData$intensity) + scale_x_continuous('', expand=c(0,0), breaks=parentData$retention)
} else {}
dev.set(device)
print(p)
if(ionTrace){
vp <- viewport(width=0.4, height=0.3, x=0.98, y=0.98, just=c('right', 'top'))
print(q, vp=vp)
}
}
collectRawPlotSettings <- function(){
ans <- list()
ans$ppm <- as.numeric(ppmPlotSetting$getText())
ans$neutralLosses <- neutralPlotSetting$getActive()
ans$ionTrace <- tracePlotSetting$getActive()
ans$ions <- paste(if(aIonPlotSetting$getActive()) 'a', if(bIonPlotSetting$getActive()) 'b', if(cIonPlotSetting$getActive()) 'c', if(xIonPlotSetting$getActive()) 'x', if(yIonPlotSetting$getActive()) 'y', if(zIonPlotSetting$getActive()) 'z', sep='')
ans
}
getRunInfoFromMZID <- function(file){
parsedMZID <- xmlTreeParse(file, useInternalNodes=TRUE)
rootMZID <- xmlRoot(parsedMZID)
database <- xmlAttrs(rootMZID[['DataCollection']][['Inputs']][['SearchDatabase']])['location']
if(!file.exists(database)){
database <- file.path(dirname(file), basename(database))
if(!file.exists(database)){
database <- NA
} else {}
} else {}
rawfile <- xmlAttrs(rootMZID[['DataCollection']][['Inputs']][['SpectraData']])['location']
if(!file.exists(rawfile)){
rawfile <- file.path(dirname(file), basename(rawfile))
if(!file.exists(rawfile)){
rawfile <- NA
} else {}
} else {}
resultfile <- file
analysisPar <- list()
for(i in 1:length(xmlSApply(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['AdditionalSearchParams']], xmlName))){
if(xmlName(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['AdditionalSearchParams']][[i]]) == 'userParam'){
param <- xmlAttrs(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['AdditionalSearchParams']][[i]])
if(param['name'] == 'TargetDecoyApproach'){
analysisPar$tda <- as.logical(param['value'])
} else if(param['name'] == 'MinIsotopeError'){
analysisPar$isotopeError[1] <- as.numeric(param['value'])
} else if(param['name'] == 'MaxIsotopeError'){
analysisPar$isotopeError[2] <- as.numeric(param['value'])
} else if(param['name'] == 'FragmentMethod'){
analysisPar$fragmentation <- param['value']
} else if(param['name'] == 'Instrument'){
analysisPar$instrument <- param['value']
} else if(param['name'] == 'NumTolerableTermini'){
analysisPar$termini <- as.numeric(param['value'])
} else if(param['name'] == 'NumMatchesPerSpec'){
analysisPar$matches <- as.numeric(param['value'])
} else if(param['name'] == 'MinPepLength'){
analysisPar$lengthRange[1] <- as.numeric(param['value'])
} else if(param['name'] == 'MaxPepLength'){
analysisPar$lengthRange[2] <- as.numeric(param['value'])
} else if(param['name'] == 'MinCharge'){
analysisPar$chargeRange[1] <- as.numeric(param['value'])
} else if(param['name'] == 'MaxCharge'){
analysisPar$chargeRange[2] <- as.numeric(param['value'])
} else {}
} else {}
}
analysisPar$protease <- xmlAttrs(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['Enzymes']][['Enzyme']][['EnzymeName']][['cvParam']])['name']
analysisPar$tolerance <- as.numeric(xmlAttrs(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['ParentTolerance']][['cvParam']])['value'])
tolUnit <- xmlAttrs(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['ParentTolerance']][['cvParam']])['unitName']
if(tolower(tolUnit) == 'parts per million'){
analysisPar$tolerance <- paste(analysisPar$tolerance, 'ppm', sep='')
} else if(tolower(tolUnit) == 'dalton'){
analysisPar$tolerance <- paste(analysisPar$tolerance, 'Da', sep='')
} else {
analysisPar$tolerance <- as.character(analysisPar$tolerance)
}
free(parsedMZID)
list(database=database, rawfile=rawfile, resultfile=resultfile, parameters=analysisPar)
}
updateSampleList <- function(add){
newSample <- data.frame(Samples=basename(add$rawfile), '.notAll'=TRUE, loaded=FALSE, database=add$database, rawfile=add$rawfile, resultfile=add$resultfile, check.names=FALSE, stringsAsFactors=FALSE)
if(any(samples[,'Samples'] %in% newSample$Samples)){
} else {}
samples$appendRows(newSample)
}
findProteinSequence <- function(name){
rawfiles <- unique(as.character(rawResults[rawResults[,'Protein'] == name, 1]))
databases <- unique(samples[samples[, 'Samples'] %in% rawfiles, 'database'])
seq <- list()
for(i in 1:length(databases)){
seqs <- readAAStringSet(databases[i])
ans <- list(sequence=as.character(seqs[which(sapply(strsplit(names(seqs), ' '), '[', 1) == name)]), files=samples[which(samples[, 'database'] == databases[i]), 'Samples'])
seq[[i]] <- ans
}
seq
}
findProteinEvidence <- function(name, sample, FDR){
if(missing(sample)){
ind <- which(rawResults[, 'Protein'] == name & rawResults[, 'QValue'] <= FDR)
ans <- rawResults[ind, 'realPeptide']
} else {
ind <- which(rawResults[, 'Protein'] == name & rawResults[, 'SpecFile'] == sample & rawResults[, 'QValue'] <= FDR)
ans <- rawResults[ind, 'realPeptide']
}
split(ind, ans)
}
findProteinEvidenceLocation <- function(sequence, evidence, collate=TRUE){
ans <- list()
for(i in 1:length(evidence)){
m <- regexpr(names(evidence)[i], sequence)
ans[[i]] <- c(m, m+attr(m, 'match.length')-1)
}
if(collate){
m <- sort(unique(unlist(lapply(ans, function(x) seq(x[1], x[2])))))
d <- diff(m)
d1 <- which(d != 1)
ans <- list()
if(length(d1) == 0){
ans[[1]] <- c(m[1], m[length(m)])
} else {
ans[[1]] <- c(m[1], m[d1[1]])
if(length(d1) > 1){
for(i in 2:length(d1)){
ans[[i]] <- c(m[d1[i-1]+1], m[d1[i]])
}
}
ans[[length(ans)+1]] <- c(m[d1[length(d1)]+1], m[length(m)])
}
} else {}
ans
}
formatProteinPango <- function(sequence, evidence, evidenceHighlight, breakPosition=40){
markupLocation <- findProteinEvidenceLocation(sequence, evidence, collate=TRUE)
if(!missing(evidenceHighlight)){
highlightLocation <- findProteinEvidenceLocation(sequence, evidence[evidenceHighlight], collate=FALSE)
}
sequence <- strsplit(sequence, '')[[1]]
ans <- c()
if(markupLocation[[1]][1] != 1){
ans <- paste(sequence[1:(markupLocation[[1]][1]-1)], collapse='')
} else {
ans <- c()
}
for(i in 1:length(markupLocation)){
if(!missing(evidenceHighlight) && markupLocation[[i]][1] <= highlightLocation[[1]][1] && markupLocation[[i]][2] >= highlightLocation[[1]][2]){
if(markupLocation[[i]][1] != highlightLocation[[1]][1]) ans <- paste(ans, '<span color=\'#B64926\'>', paste(sequence[markupLocation[[i]][1]:(highlightLocation[[1]][1]-1)], collapse=''), '</span>', sep='')
ans <- paste(ans, '<span bgcolor=\'#468966\'>', paste(sequence[highlightLocation[[1]][1]:highlightLocation[[1]][2]], collapse=''), '</span>', sep='')
if(markupLocation[[i]][2] != highlightLocation[[1]][2]) ans <- paste(ans, '<span color=\'#B64926\'>', paste(sequence[(highlightLocation[[1]][2]+1):markupLocation[[i]][2]], collapse=''), '</span>', sep='')
} else {
ans <- paste(ans, '<span color=\'#B64926\'>', paste(sequence[markupLocation[[i]][1]:markupLocation[[i]][2]], collapse=''), '</span>', sep='')
}
if(i != length(markupLocation)){
ans <- paste(ans, paste(sequence[(markupLocation[[i]][2]+1):(markupLocation[[i+1]][1]-1)], collapse=''), sep='')
}
}
if(markupLocation[[length(markupLocation)]][2] < length(sequence)){
ans <- paste(ans, paste(sequence[(markupLocation[[length(markupLocation)]][2]+1):length(sequence)], collapse=''), sep='')
}
if(breakPosition > 0 & breakPosition < length(sequence)){
seqSplitted <- regmatches(ans, gregexpr('<.*?>', ans, perl=T), invert=TRUE)
if(length(which(seqSplitted[[1]] == '') != 0)) {
addEmpty <- which(seqSplitted[[1]] == '')
seqSplitted[[1]] <- seqSplitted[[1]][-which(seqSplitted[[1]] == '')]
} else {
addEmpty <- c()
}
splitPosition <- split(rep(1:ceiling(length(sequence)/breakPosition), each=breakPosition)[1:length(sequence)], rep(1:length(seqSplitted[[1]]), nchar(seqSplitted[[1]])))
lineBreakInsert <- mapply(function(x, y) paste(unlist(sapply(split(x, y), function(x) c(x, '\n'))), collapse=''), strsplit(seqSplitted[[1]], ''), splitPosition)
for(i in 1:(length(lineBreakInsert)-1)){
if(splitPosition[[i]][length(splitPosition[[i]])] == splitPosition[[i+1]][1]){
lineBreakInsert[[i]] <- sub('\n$', '', lineBreakInsert[[i]], perl=T)
} else {}
}
lineBreakInsert[[length(lineBreakInsert)]] <- sub('\n$', '', lineBreakInsert[[length(lineBreakInsert)]], perl=T)
if(length(addEmpty) > 0){
for(i in addEmpty){
lineBreakInsert <- append(lineBreakInsert, '', i-1)
}
}
lineBreakInsert <- list(lineBreakInsert)
regmatches(ans, gregexpr('<.*?>', ans, perl=T), invert=TRUE) <- lineBreakInsert
}
ans
}
blastPut <- function(seq, db, ...){
### Based on blast.pdb
urlput <- paste("http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Put&DATABASE=", db,"&PROGRAM=blastp&CLIENT=web&QUERY=", seq, sep="")
txt <- scan(urlput, what="raw", sep="\n", quiet=TRUE)
rid <- sub("^.*RID = " ,"",txt[ grep("RID =",txt) ])
rid
}
blastCheck <- function(rid){
urlget <- paste("http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=",rid, sep="")
txt <- scan(urlget, what="raw", sep="\n", quiet=TRUE)
status <- sub("^.*Status=" ,"",txt[ grep("Status=",txt) ])
status
}
blastGet <- function(rid, browser=TRUE, ...){
urlget <- paste("http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=",rid, sep="")
if(browser){
browseURL(urlget)
}
}
formatPeptideSequence <- function(seq){
ans <- strsplit(seq, '.', fixed=T)[[1]]
ans <- paste(sub('-', '|', ans), collapse='--')
modPos <- c()
mod <- c()
while(1){
mods <- regexpr('\\+([\\d]|,)+', ans, perl=TRUE)
if(mods == -1){
break
} else {
modPos <- c(modPos, mods-1)
mod <- c(mod, regmatches(ans, mods))
regmatches(ans, mods) <- ''
}
}
top <- list(rep(' ', nchar(ans)), rep(' ', nchar(ans)))
bottom <- list(rep(' ', nchar(ans)), rep(' ', nchar(ans)))
if(length(modPos) > 0){
mod <- sub('+', '', mod, fixed=TRUE)
mod <- sub(',', '.', mod, fixed=TRUE)
for(i in length(modPos):1){
start <- 2
while(1){
if(start > length(top)){
top <- c(top, list(rep(' ', nchar(ans))))
} else {}
if(start > length(bottom)){
bottom <- c(bottom, list(rep(' ', nchar(ans))))
} else {}
if(all(top[[start]][modPos[i]:(modPos[i]+nchar(mod[i])-1)] == ' ', na.rm=TRUE)){
top[[start]][modPos[i]:(modPos[i]+nchar(mod[i])-1)] <- strsplit(mod, '')[[1]]
retract <- start-1
while(retract){
top[[retract]][modPos[i]] <- '|'
retract <- retract-1
}
break
} else if(all(bottom[[start]][modPos[i]:(modPos[i]+nchar(mod[i])-1)] == ' ', na.rm=TRUE)){
bottom[[start]][modPos[i]:(modPos[i]+nchar(mod[i])-1)] <- strsplit(mod, '')[[1]]
retract <- start-1
while(retract){
bottom[[retract]][modPos[i]] <- '|'
retract <- retract-1
}
break
} else {
start <- start+1
}
}
}
} else {}
top <- paste(sapply(top, paste, collapse=''), '\n', sep='')
bottom <- paste(sapply(bottom, paste, collapse=''), '\n', sep='')
ans <- c(rev(top), paste(ans, '\n', sep=''), bottom)
ans
}
createPeptideView <- function(seq){
VBox <- gtkVBox(FALSE, 5)
VBox['border-width'] <- 5
alternativeRawSeq <- unique(rawResults[rawResults[,'realPeptide'] == seq & rawResults[,'.vis'], 'Peptide'])
for(i in alternativeRawSeq){
if(i != alternativeRawSeq[1]){
separator <- gtkHSeparatorNew()
separator['height-request'] <- 30
VBox$packStart(separator, expand=FALSE, fill=FALSE)
}
peptideOverview <- gtkLabel(paste(formatPeptideSequence(i), collapse=''))
font_descr <- pangoFontDescriptionNew()
font_descr$setFamily('courier')
peptideOverview$modifyFont(font_descr)
peptideOverviewScroll <- gtkScrolledWindow()
peptideOverviewScroll$setPolicy(hscrollbar.policy=GtkPolicyType[2], vscrollbar.policy=GtkPolicyType[3])
peptideOverviewScroll$addWithViewport(peptideOverview)
peptideOverviewScroll$getChild()$setShadowType(GtkShadowType[1])
VBox$packStart(peptideOverviewScroll, expand=FALSE, fill=FALSE)
peptideViewTable <- gtkTable()
peptideViewTable['border-width'] <- 5
nDetectionLabel <- gtkLabel('Number of times detected:')
nDetectionLabel['xalign'] <- 1
peptideViewTable$attach(nDetectionLabel, left.attach=0,1, top.attach=0,1)
nDetectionValue <- gtkLabel(sum(rawResults[,'Peptide'] == i & rawResults[,'.vis']))
nDetectionValue['xalign'] <- 0
peptideViewTable$attach(nDetectionValue, left.attach=1,2, top.attach=0,1)
pepLengthLabel <- gtkLabel('Length (residues):')
pepLengthLabel['xalign'] <- 1
peptideViewTable$attach(pepLengthLabel, left.attach=0,1, top.attach=1,2)
pepLengthValue <- gtkLabel(nchar(seq))
pepLengthValue['xalign'] <- 0
peptideViewTable$attach(pepLengthValue, left.attach=1,2, top.attach=1,2)
pepMassLabel <- gtkLabel('Mass:')
pepMassLabel['xalign'] <- 1
peptideViewTable$attach(pepMassLabel, left.attach=0,1, top.attach=2,3)
pepMassValue <- gtkLabel(paste(sprintf('%.2f', pepMass(seq)), 'Da'))
pepMassValue['xalign'] <- 0
peptideViewTable$attach(pepMassValue, left.attach=1,2, top.attach=2,3)
pepPILabel <- gtkLabel('Isoelectric point (pI):')
pepPILabel['xalign'] <- 1
peptideViewTable$attach(pepPILabel, left.attach=0,1, top.attach=3,4)
pepPIValue <- gtkLabel(sprintf('%.2f', peppI(seq)))
pepPIValue['xalign'] <- 0
peptideViewTable$attach(pepPIValue, left.attach=1,2, top.attach=3,4)
hydroPepLabel <- gtkLabel('Hydrophobicity (Q Value):')
hydroPepLabel['xalign'] <- 1
peptideViewTable$attach(hydroPepLabel, left.attach=0,1, top.attach=4,5)
hydroPepValue <- gtkLabel(sprintf('%.1f', Qval(seq)))
hydroPepValue['xalign'] <- 0
peptideViewTable$attach(hydroPepValue, left.attach=1,2, top.attach=4,5)
peptideViewTable$setRowSpacings(15)
peptideViewTable$setColSpacings(5)
VBox$packStart(peptideViewTable, expand=FALSE, fill=FALSE)
peptideDF <- rawResults[rawResults[,'Peptide'] == i & rawResults[,'.vis'], ]
peptideViewModel <- gtkTreeStore('gchararray', 'gchararray', 'gchararray')
by(peptideDF, peptideDF$Protein, function(x){
parent_iter <- peptideViewModel$append()
peptideViewModel$setValue(parent_iter$iter, column=0, paste('Protein: ', x$Protein[1], sep=''))
by(x, x$SpecFile, function(y){
parent2_iter <- peptideViewModel$append(parent=parent_iter$iter)
peptideViewModel$setValue(parent2_iter$iter, column=0, paste('Sample: ', y$SpecFile[1], sep=''))
by(y, y$Charge, function(z){
parent3_iter <- peptideViewModel$append(parent=parent2_iter$iter)
peptideViewModel$setValue(parent3_iter$iter, column=0, paste('Charge: ', z$Charge[1], sep=''))
for(i in 1:nrow(z)){
child_iter <- peptideViewModel$append(parent=parent3_iter$iter)
peptideViewModel$setValue(child_iter$iter, column=1, value=z[i, 'ScanNum'])
peptideViewModel$setValue(child_iter$iter, column=2, value=z[i, 'QValue'])
}
})
})
})
peptideTreeView <- gtkTreeView()
peptideTreeView$insertColumnWithAttributes(-1, '', gtkCellRendererText(), text=0)
peptideTreeView$insertColumnWithAttributes(-1, 'Scan Number', gtkCellRendererText(), text=1)
peptideTreeView$insertColumnWithAttributes(-1, 'FDR', gtkCellRendererText(), text=2)
peptideTreeView$setModel(peptideViewModel)
peptideTreeViewScroll <- gtkScrolledWindow()
peptideTreeView['height-request'] <- 200
peptideTreeViewScroll$add(peptideTreeView)
peptideTreeSelection <- peptideTreeView$getSelection()
gSignalConnect(peptideTreeView, 'row-activated', function(...){
if(!with(peptideTreeSelection$getSelected(), model$iterParent(iter)$retval)){
proteinName <- with(peptideTreeSelection$getSelected(), model$getValue(iter, 0)$value)
proteinName <- sub('Protein: ', '', proteinName)
proteinPath <- gtkTreePathNewFromString(which(proteins[] == proteinName)-1)
resultNotebook$setCurrentPage(resultNotebook$pageNum(proteinTab))
proteinSelect$selectPath(proteinPath)
protein$scrollToCell(proteinPath, use.align=TRUE, row.align=0.5)
gSignalEmit(protein, 'cursor-changed')
} else if(!with(peptideTreeSelection$getSelected(), model$iterHasChild(iter))){
scanNum <- with(peptideTreeSelection$getSelected(), model$getValue(iter, 1)$value)
sample <- sub('Sample: ', '', with(peptideTreeSelection$getSelected(), with(model$iterParent(model$iterParent(iter)$iter), model$getValue(iter, 0)$value)))
proteinName <- sub('Protein: ', '', with(peptideTreeSelection$getSelected(), with(model$iterParent(model$iterParent(model$iterParent(iter)$iter)$iter), model$getValue(iter, 0)$value)))
ind <- which(rawResults[,'SpecFile'] == sample & rawResults[,'ScanNum'] == scanNum & rawResults[,'Protein'] == proteinName)
if(length(ind) == 1){
rawPath <- gtkTreePathNewFromString(ind-1)
resultNotebook$setCurrentPage(resultNotebook$pageNum(rawTab))
rawSelect$selectPath(rawPath)
raw$scrollToCell(rawPath)
raw$rowActivated(rawPath, gtkTreeViewColumn())
}
}
})
VBox$packStart(peptideTreeViewScroll, expand=FALSE, fill=FALSE)
}
viewportVBox <- gtkViewport()
viewportVBox$add(VBox)
viewportVBox$setShadowType(GtkShadowType[1])
return(viewportVBox)
}
mainWindow <- gtkWindow(show=FALSE)
mainWindow$setTitle('MS GF+')
topGroup <- gtkVBox(FALSE, 5)
mainWindow$add(topGroup)
toolbar <- gtkToolbar()
topGroup$packStart(toolbar, expand=FALSE)
importAction <- gtkAction(name='import', label='Import', tooltip='Import mzIdentML files', stock.id='gtk-add')
gSignalConnect(importAction, 'activate', f=function(...){
file <- gtkFileChooserDialog(title='Select MS datafiles', parent=NULL, action='open', 'gtk-ok', GtkResponseType['ok'], 'gtk-cancel', GtkResponseType['cancel'], show=FALSE)
file['select-multiple'] <- TRUE
gSignalConnect(file, 'response', f=function(dialog, response, data){
dialog$hide()
})
response <- file$Run()
if(response == GtkResponseType["ok"]){
filenames <- unlist(file$getFilenames())
for(i in 1:length(filenames)){
if(Sys.info()["sysname"] == 'Windows'){
filename <- paste('\"', filenames[i], '\"', sep='')
} else {
filename <- gsub(' ', '\\ ', filenames[i], fixed=T)
}
callConv <- paste('java -Xmx', 10000, 'M -cp ', R.home(component='library/pepmaps/java/MSGFplus.jar'), ' edu.ucsd.msjava.ui.MzIDToTsv -i ', filename, ' -o ', paste(filename, '.tsv', sep=''), ' -unroll 1 -showDecoy 1', sep='')
system(callConv)
if(length(scan(paste(filenames[i], '.tsv', sep=''), skip=1, nlines=1, what='character', quiet=T)) != 0){
results <- read.table(paste(filenames[i], '.tsv', sep=''), sep='\t', header=TRUE, comment.char='', stringsAsFactors=FALSE)
names(results) <- sub('#', '', scan(paste(filenames[i], '.tsv', sep=''), nlines=1, what=character(), quiet=TRUE))
unlink(paste(filenames[i], '.tsv', sep=''))
sNum <- regexpr('scanId=[\\d]+', results$SpecID, perl=TRUE)
sNum <- substr(results$SpecID, sNum, sNum+attr(sNum, 'match.length')-1)
sNum <- sub('scanId=', '', sNum)
results$ScanNum <- sNum
peptide <- strsplit(as.character(results$Peptide), '\\.')
peptide <- unlist(peptide)[seq(2, length(peptide)*3, by=3)]
peptide <- gsub('\\+([\\d]|,)+', '', peptide, perl=TRUE)
results$realPeptide <- peptide
results$'.vis' <- rawFilter(results, sample=sampleFilter(), FDR=FDR$getValue())
rawResults$appendRows(results)
rawUpdated()
sampleInfo <- getRunInfoFromMZID(filenames[i])
updateSampleList(add=sampleInfo)
} else {}
}
} else {}
file$destroy()
})
importToolButton <- importAction$createToolItem()
toolbar$add(importToolButton)
removeAction <- gtkAction(name='remove', label='Remove', tooltip='Remove analysis results', stock.id='gtk-remove')
gSignalConnect(removeAction, 'activate', f=function(...){
removeDialog <- gtkDialogNewWithButtons(title='Remove sample results', parent=mainWindow, flags=1, 'Remove', GtkResponseType['ok'], 'Cancel', GtkResponseType['cancel'], show=FALSE)
removeDialogContent <- removeDialog$getContentArea()
removeDialogScroll <- gtkScrolledWindow()
removeDialogContent$packStart(removeDialogScroll)
removeDialogList <- gtkTreeView(samplesFilter)
removeDialogList$insertColumnWithAttributes(position=-1, title='MS datafiles', cell=gtkCellRendererText(), text=0)
removeDialogList$setHeadersVisible(FALSE)
removeDialogList['height-request'] <- 100
removeDialogSelect <- removeDialogList$getSelection()
removeDialogSelect$setMode('multiple')
removeDialogScroll$add(removeDialogList)
gSignalConnect(removeDialog, 'response', f=function(dialog, response, ...){
if(response == GtkResponseType['ok']){
samplesToRemoveIndex <- sapply(removeDialogSelect$getSelectedRows()$retval, function(x) as.numeric(samplesFilter$convertPathToChildPath(x)$toString())+1)
samplesToRemove <- samples[samplesToRemoveIndex, 1]
allIndex <- which(samplesToRemove == 'All')
if(length(allIndex) != 0){
samplesToRemoveIndex <- samplesToRemoveIndex[-allIndex]
samplesToRemove <- samplesToRemove[-allIndex]
}
rawRowsToRemove <- which(rawResults[,'SpecFile'] %in% samplesToRemove)
samples$setFrame(data.frame(samples[-samplesToRemoveIndex, , drop=FALSE]))
rawResults$setFrame(data.frame(rawResults[-rawRowsToRemove, , drop=FALSE]))
rawUpdated()
}
dialog$Destroy()
})
removeDialog$show()
})
removeToolButton <- removeAction$createToolItem()
toolbar$add(removeToolButton)
exportAction <- gtkAction(name='export', label='Export', tooltip='Export results', stock.id='gtk-save')
exportToolButton <- exportAction$createToolItem()
toolbar$add(exportToolButton)
toolbar$add(gtkSeparatorToolItem())
sampleInfoAction <- gtkAction(name='sample.info', label='Samples', tooltip='View sample information', stock.id='gtk-info')
sampleInfoToolButton <- sampleInfoAction$createToolItem()
toolbar$add(sampleInfoToolButton)
mainGroup <- gtkHBox(FALSE, 5)
mainGroup$setBorderWidth(5)
topGroup$packStart(mainGroup)
controlGroup <- gtkVBox(FALSE, 5)
mainGroup$packStart(controlGroup, expand=FALSE, fill=FALSE)
importFrame <- gtkFrame('Data files to use')
controlGroup$packStart(importFrame)
importBox <- gtkVBox(FALSE, 5)
importBox$setBorderWidth(5)
importFrame$add(importBox)
datafileSelect <- gtkHBox(FALSE, 5)
importBox$packStart(datafileSelect)
filesScroll <- gtkScrolledWindow()
datafileSelect$packStart(filesScroll)
files <- gtkTreeView(filelist)
files$insertColumnWithAttributes(position=-1, title='MS datafiles', cell=gtkCellRendererText(), text=0)
files$setHeadersVisible(FALSE)
files['height-request'] <- 100
fileSelect <- files$getSelection()
fileSelect$setMode('multiple')
filesScroll$add(files)
datafileSelectButtons <- gtkVBox(FALSE, 5)
datafileSelect$packStart(datafileSelectButtons, expand=FALSE, fill=FALSE)
fileAddButton <- gtkButton(label='Add')
fileAddButton['width-request'] <- 65
gSignalConnect(fileAddButton, 'clicked', f=function(widget, ...){
file <- gtkFileChooserDialog(title='Select MS datafiles', parent=mainWindow, action='open', 'gtk-ok', GtkResponseType['ok'], 'gtk-cancel', GtkResponseType['cancel'], show=FALSE)
file['select-multiple'] <- TRUE
gSignalConnect(file, 'response', f=function(dialog, response, data){
if(response == GtkResponseType['ok']){
files <- as.character(dialog$getFilenames())
filelist$appendRows(data.frame(Datafiles=files, stringsAsFactors=FALSE))
setwd(dirname(files[1]))
}
dialog$destroy()
})
file$show()
})
fileRemoveButton <- gtkButton(label='Remove')
fileRemoveButton['width-request'] <- 65
fileRemoveButton['sensitive'] <- FALSE
gSignalConnect(fileRemoveButton, 'clicked', f=function(widget, ...){
selected <- sapply(fileSelect$getSelectedRows()$retval, function(x) as.numeric(x$toString())+1)
filelist$setFrame(filelist[-selected, , drop=FALSE])
})
datafileSelectButtons$packStart(fileAddButton, expand=FALSE, fill=FALSE)
datafileSelectButtons$packStart(fileRemoveButton, expand=FALSE, fill=FALSE)
databaseSelect <- gtkHBox(FALSE, 5)
importBox$packStart(databaseSelect, expand=FALSE, fill=FALSE)
database <- gtkEntry()
database['height-request'] <- 24
database$setText('Database fasta file...')
gSignalConnect(database, 'changed', f=function(widget, ...){
validButtons()
})
databaseImport <- gtkButton(label='Browse')
databaseImport['width-request'] <- 65
gSignalConnect(databaseImport, 'clicked', f=function(widget, ...){
file <- gtkFileChooserDialog(title='Select MS datafiles', parent=mainWindow, action='open', 'gtk-ok', GtkResponseType['ok'], 'gtk-cancel', GtkResponseType['cancel'], show=FALSE)
gSignalConnect(file, 'response', f=function(dialog, response, data){
if(response == GtkResponseType['ok']){
file <- as.character(dialog$getFilenames())
database$setText(file)
}
dialog$destroy()
})
file$show()
})
databaseSelect$packStart(database)
databaseSelect$packStart(databaseImport, expand=FALSE, fill=FALSE)
settingsFrame <- gtkFrame('Settings')
controlGroup$packStart(settingsFrame, expand=FALSE, fill=FALSE)
settingsBox <- gtkVBox(FALSE, 15)
settingsBox$setBorderWidth(5)
settingsFrame$add(settingsBox)
settingsSet <- gtkHBox(FALSE, 5)
settingsBox$packStart(settingsSet, expand=FALSE, fill=FALSE)
settingsSetChooser <- gtkComboBoxNewText()
sapply(settingsSetNames, settingsSetChooser$appendText)
settingsSetSaveButton <- gtkButton(label='Save')
settingsSetSaveButton['width-request'] <- 65
settingsSet$packStart(settingsSetChooser)
settingsSet$packStart(settingsSetSaveButton, expand=FALSE, fill=FALSE)
settingsTable <- gtkTable(rows=11, columns=2, homogeneous=FALSE)
settingsTable$setColSpacings(10)
settingsTable$setRowSpacings(10)
settingsBox$packStart(settingsTable)
toleranceLabel <- gtkLabel('Tolerance:')
toleranceLabel['xalign'] <- 1
settingsTable$attach(toleranceLabel, left.attach=0,1, top.attach=0,1)
toleranceBox <- gtkHBox(FALSE, 5)
toleranceValue <- gtkEntry()
toleranceValue['height-request'] <- 24
toleranceValue['width-chars'] <- 5
toleranceValue$setAlignment(1)
toleranceValue$setText(20)
toleranceUnit <- gtkComboBoxNewText()
sapply(c('ppm', 'Da'), toleranceUnit$appendText)
toleranceUnit$setActive(0)
toleranceBox$packStart(toleranceValue, expand=FALSE, fill=FALSE)
toleranceBox$packStart(toleranceUnit, expand=FALSE, fill=FALSE)
settingsTable$attach(toleranceBox, left.attach=1,2, top.attach=0,1)
isotopeErrorLabel <- gtkLabel('Isotope error range:')
isotopeErrorLabel['xalign'] <- 1
settingsTable$attach(isotopeErrorLabel, left.attach=0,1, top.attach=1,2)
isotopeErrorBox <- gtkHBox(FALSE, 5)
isotopeErrorLow <- gtkSpinButton(min=-5, max=10, step=1)
isotopeErrorLow['height-request'] <- 24
isotopeErrorLow['width-chars'] <- 3
isotopeErrorLow$setAlignment(1)
isotopeErrorLow$setValue(0)
gSignalConnect(isotopeErrorLow, 'value-changed', f=function(widget, ...){
min <- widget$getValue()
if(min > isotopeErrorHigh$getValue()){
isotopeErrorHigh$setRange(min, 10)
}
})
isotopeErrorHigh <- gtkSpinButton(min=0, max=10, step=1)
isotopeErrorHigh['height-request'] <- 24
isotopeErrorHigh['width-chars'] <- 3
isotopeErrorHigh$setAlignment(1)
isotopeErrorHigh$setValue(1)
isotopeErrorBox$packStart(isotopeErrorLow, expand=FALSE, fill=FALSE)
isotopeErrorBox$packStart(gtkLabel(' - '), expand=FALSE, fill=FALSE)
isotopeErrorBox$packStart(isotopeErrorHigh, expand=FALSE, fill=FALSE)
settingsTable$attach(isotopeErrorBox, left.attach=1,2, top.attach=1,2)
tdaLabel <- gtkLabel('Target-Decoy:')
tdaLabel['xalign'] <- 1
settingsTable$attach(tdaLabel, left.attach=0,1, top.attach=2,3)
tdaToggle <- gtkCheckButton()
tdaToggle$setActive(TRUE)
settingsTable$attach(tdaToggle, left.attach=1,2, top.attach=2,3)
fragmentationLabel <- gtkLabel('Fragmentation method:')
fragmentationLabel['xalign'] <- 1
settingsTable$attach(fragmentationLabel, left.attach=0,1, top.attach=3,4)
fragmentation <- gtkComboBoxNewText()
sapply(c('From spectrum', 'CID', 'ETD', 'HCD', 'Merge'), fragmentation$appendText)
fragmentation$setActive(0)
settingsTable$attach(fragmentation, left.attach=1,2, top.attach=3,4)
instrumentLabel <- gtkLabel('Instrument:')
instrumentLabel['xalign'] <- 1
settingsTable$attach(instrumentLabel, left.attach=0,1, top.attach=4,5)
instrument <- gtkComboBoxNewText()
sapply(c('Low-res LCQ/LTQ', 'High-res LTQ', 'TOF'), instrument$appendText)
instrument$setActive(0)
settingsTable$attach(instrument, left.attach=1,2, top.attach=4,5)
enzymeLabel <- gtkLabel('Enzyme:')
enzymeLabel['xalign'] <- 1
settingsTable$attach(enzymeLabel, left.attach=0,1, top.attach=5,6)
enzyme <- gtkComboBoxNewText()
sapply(c('Unspecific', 'Trypsin', 'Chymotrypsin', 'Lys-C', 'Lys-N', 'Glu-C', 'Arg-C', 'Asp-N', 'alphaLP', 'None'), enzyme$appendText)
enzyme$setActive(1)
settingsTable$attach(enzyme, left.attach=1,2, top.attach=5,6)
terminiLabel <- gtkLabel('Tolerable termini:')
terminiLabel['xalign'] <- 1
settingsTable$attach(terminiLabel, left.attach=0,1, top.attach=6,7)
terminiBox <- gtkHBox(FALSE, 5)
termini <- gtkSpinButton(min=0, max=2, step=1)
termini$setValue(2)
termini['height-request'] <- 24
termini['width-chars'] <- 3
termini$setAlignment(1)
terminiBox$packStart(termini, expand=FALSE, fill=FALSE)
settingsTable$attach(terminiBox, left.attach=1,2, top.attach=6,7)
modificationLabel <- gtkLabel('Custom modification file:')
modificationLabel['xalign'] <- 1
settingsTable$attach(modificationLabel, left.attach=0,1, top.attach=7,8)
modificationBox <- gtkHBox(FALSE, 5)
modification <- gtkEntry()
modification['height-request'] <- 24
modification['width-chars'] <- 15
modification$setText('Modification file...')
gSignalConnect(modification, 'changed', f=function(widget, ...){
validButtons()
})
modificationImport <- gtkButton(label='Browse')
modificationImport['width-request'] <- 65
gSignalConnect(modificationImport, 'clicked', f=function(widget, ...){
file <- gtkFileChooserDialog(title='Select MS datafiles', parent=mainWindow, action='open', 'gtk-ok', GtkResponseType['ok'], 'gtk-cancel', GtkResponseType['cancel'], show=FALSE)
gSignalConnect(file, 'response', f=function(dialog, response, data){
if(response == GtkResponseType['ok']){
file <- as.character(dialog$getFilenames())
modification$setText(file)
}
dialog$destroy()
})
file$show()
})
modificationBox$packStart(modification)
modificationBox$packStart(modificationImport, expand=FALSE, fill=FALSE)
settingsTable$attach(modificationBox, left.attach=1,2, top.attach=7,8)
lengthLabel <- gtkLabel('Peptide length:')
lengthLabel['xalign'] <- 1
settingsTable$attach(lengthLabel, left.attach=0,1, top.attach=8,9)
lengthBox <- gtkHBox(FALSE, 5)
lengthLow <- gtkSpinButton(min=1, max=100, step=1)
lengthLow['height-request'] <- 24
lengthLow['width-chars'] <- 3
lengthLow$setAlignment(1)
lengthLow$setValue(6)
gSignalConnect(lengthLow, 'value-changed', f=function(widget, ...){
min <- widget$getValue()
if(min > lengthHigh$getValue()){
lengthHigh$setRange(min, 100)
}
})
lengthHigh <- gtkSpinButton(min=6, max=100, step=1)
lengthHigh['height-request'] <- 24
lengthHigh['width-chars'] <- 3
lengthHigh$setAlignment(1)
lengthHigh$setValue(40)
lengthBox$packStart(lengthLow, expand=FALSE, fill=FALSE)
lengthBox$packStart(gtkLabel(' - '), expand=FALSE, fill=FALSE)
lengthBox$packStart(lengthHigh, expand=FALSE, fill=FALSE)
settingsTable$attach(lengthBox, left.attach=1,2, top.attach=8,9)
chargeLabel <- gtkLabel('Peptide charge:')
chargeLabel['xalign'] <- 1
settingsTable$attach(chargeLabel, left.attach=0,1, top.attach=9,10)
chargeBox <- gtkHBox(FALSE, 5)
chargeLow <- gtkSpinButton(min=1, max=10, step=1)
chargeLow['height-request'] <- 24
chargeLow['width-chars'] <- 3
chargeLow$setAlignment(1)
chargeLow$setValue(2)
gSignalConnect(chargeLow, 'value-changed', f=function(widget, ...){
min <- widget$getValue()
if(min > chargeHigh$getValue()){
chargeHigh$setRange(min, 10)
}
})
chargeHigh <- gtkSpinButton(min=2, max=10, step=1)
chargeHigh['height-request'] <- 24
chargeHigh['width-chars'] <- 3
chargeHigh$setAlignment(1)
chargeHigh$setValue(3)
chargeBox$packStart(chargeLow, expand=FALSE, fill=FALSE)
chargeBox$packStart(gtkLabel(' - '), expand=FALSE, fill=FALSE)
chargeBox$packStart(chargeHigh, expand=FALSE, fill=FALSE)
settingsTable$attach(chargeBox, left.attach=1,2, top.attach=9,10)
matchLabel <- gtkLabel('Matches per spectrum:')
matchLabel['xalign'] <- 1
settingsTable$attach(matchLabel, left.attach=0,1, top.attach=10,11)
matchBox <- gtkHBox(FALSE, 5)
match <- gtkSpinButton(min=1, max=100, step=1)
match['height-request'] <- 24
match['width-chars'] <- 3
match$setAlignment(1)
matchBox$packStart(match, expand=FALSE, fill=FALSE)
settingsTable$attach(matchBox, left.attach=1,2, top.attach=10,11)
analyzeBox <- gtkHBox(FALSE, 5)
controlGroup$packStart(analyzeBox, expand=FALSE, fill=FALSE)
analyzeProgress <- gtkProgressBar()
analyzeProgress['height-request'] <- 24
analyzeBox$packStart(analyzeProgress)
analyzeButton <- gtkButton(label='Analyze')
analyzeButton['width-request'] <- 65
analyzeButton['sensitive'] <- FALSE
gSignalConnect(analyzeButton, 'clicked', f=function(widget, ...){
analyzeProgress$setFraction(0)
analyzeButton['sensitive'] <- FALSE
while(gtkEventsPending()){
gtkMainIteration()
}
datafiles <- filelist[]
settings <- collectSettings()
settings$database <- database$getText()
settings$saveMZid <- TRUE
settings$showDecoy <- TRUE
for(i in 1:length(datafiles)){
settings$file <- datafiles[i]
analyzeProgress$setText(basename(settings$file))
while(gtkEventsPending()){
gtkMainIteration()
}
results <- do.call('MSGFplus', settings)
peptide <- strsplit(as.character(results$Peptide), '\\.')
peptide <- unlist(peptide)[seq(2, length(peptide)*3, by=3)]
peptide <- gsub('\\+([\\d]|,)+', '', peptide, perl=TRUE)
results$realPeptide <- peptide
results$'.vis' <- rawFilter(results, sample=sampleFilter(), FDR=FDR$getValue())
rawResults$appendRows(results)
rawUpdated()
mzidFile <- paste(sapply(strsplit(datafiles[i],"\\."), function(x) paste(x[1:(length(x)-1)], collapse=".")), '.mzid', sep='')
sampleInfo <- getRunInfoFromMZID(mzidFile)
updateSampleList(add=sampleInfo)
analyzeProgress$setFraction(i/length(datafiles))
while(gtkEventsPending()){
gtkMainIteration()
}
}
analyzeProgress$setText('Done...')
analyzeButton['sensitive'] <- TRUE
})
analyzeBox$packStart(gtkHBox(), expand=TRUE, fill=TRUE)
analyzeBox$packStart(analyzeButton, expand=FALSE, fill=FALSE)
resultBox <- gtkVBox(FALSE, 5)
resultBox$setSensitive(FALSE)
mainGroup$packStart(resultBox)
filterFrame <- gtkFrame(label='Filters')
filterBox <- gtkHBox(FALSE, 5)
filterBox['border-width'] <- 5
filterFrame$add(filterBox)
resultBox$packStart(filterFrame, expand=FALSE, fill=TRUE)
filterBox$packStart(gtkLabel('Sample:'), expand=FALSE, fill=FALSE)
sampleSelect <- gtkComboBoxNewWithModel(samples)
sampleRenderer <- gtkCellRendererText()
sampleSelect$packStart(sampleRenderer)
sampleSelect$addAttribute(sampleRenderer, 'text', 0)
sampleSelect$setActive(0)
gSignalConnect(sampleSelect, 'changed', f=function(widget, ...){
filterUpdated(FDRChange=FALSE)
})
filterBox$packStart(sampleSelect)
filterBox$packStart(gtkHBox(), expand=TRUE, fill=TRUE)
filterBox$packStart(gtkLabel('FDR cutoff:'), expand=FALSE, fill=FALSE)
FDR <- gtkSpinButton(min=0, max=1, step=0.01)
FDR['width-chars'] <- 5
FDR['height-request'] <- 24
FDR$setValue(0.01)
gSignalConnect(FDR, 'value-changed', f=function(widget, ...){
filterUpdated(SampleChange=FALSE)
})
filterBox$packStart(FDR, expand=FALSE, fill=FALSE)
resultNotebook <- gtkNotebook()
resultNotebook['width-request'] <- 700
resultBox$packStart(resultNotebook)
summaryTab <- gtkHBox(FALSE, 5)
summaryTab['border-width'] <- 5
summaryLeft <- gtkVBox(FALSE, 5)
summaryTab$packStart(summaryLeft)
resultNotebook$appendPage(summaryTab, gtkLabel('Result summary'))
FDRplot <- gtkDrawingArea()
summaryLeft$packStart(FDRplot)
#pepNumberPlot <- gtkDrawingArea()
#summaryLeft$packStart(pepNumberPlot)
#summaryRight <- gtkVBox(FALSE, 5)
#summaryRight['width-request'] <- 100
#summaryTab$packStart(summaryRight)
summaryFrame <- gtkFrame(label='Summary')
summaryLeft$packStart(summaryFrame, expand=FALSE, fill=FALSE)
summaryTable <- gtkTable(rows=2, columns=2, homogeneous=FALSE)
summaryTable['border-width'] <- 5
summaryTable$setColSpacings(10)
summaryTable$setRowSpacings(10)
summaryFrame$add(summaryTable)
nPepIDLabel <- gtkLabel('Identified peptides:')
nPepIDLabel['xalign'] <- 1
summaryTable$attach(nPepIDLabel, left.attach=0,1, top.attach=0,1)
nPepID <- gtkLabel('')
nPepID['xalign'] <- 0
summaryTable$attach(nPepID, left.attach=1,2, top.attach=0,1)
nProtIDLabel <- gtkLabel('Identified proteins:')
nProtIDLabel['xalign'] <- 1
summaryTable$attach(nProtIDLabel, left.attach=0,1, top.attach=1,2)
nProtID <- gtkLabel('')
nProtID['xalign'] <- 0
summaryTable$attach(nProtID, left.attach=1,2, top.attach=1,2)
protIntersectLabel <- gtkLabel('Protein intersection:')
protIntersectLabel['xalign'] <- 1
summaryTable$attach(protIntersectLabel, left.attach=0,1, top.attach=2,3)
protIntersect <- gtkLabel('')
protIntersect['xalign'] <- 0
summaryTable$attach(protIntersect, left.attach=1,2, top.attach=2,3)
chargeLabel <- gtkLabel('Charge:')
chargeLabel['xalign'] <- 1
chargeLabel['yalign'] <- 0
summaryTable$attach(chargeLabel, left.attach=0,1, top.attach=3,4)
charge <- gtkLabel('\t(min)\n\t(median)\n\t(max)')
charge['xalign'] <- 0
summaryTable$attach(charge, left.attach=1,2, top.attach=3,4)
peptideTab <- gtkHBox(FALSE, 5)
peptideTab['border-width'] <- 5
peptideScroll <- gtkScrolledWindow()
peptideTab$packStart(peptideScroll)
peptide <- gtkTreeView(peptides)
peptide$insertColumnWithAttributes(position=-1, title='Peptides', cell=gtkCellRendererText(), text=0)
peptideSelection <- peptide$getSelection()
gSignalConnect(peptide, 'cursor-changed', function(...){
peptideSelected <- with(peptideSelection$getSelected(), model$getValue(iter, 0)$value)
pepInfo <- createPeptideView(peptideSelected)
if(!is.null(peptideViewScroll$getChild())) peptideViewScroll$getChild()$destroy()
peptideViewScroll$add(createPeptideView(peptideSelected))
})
peptideScroll$add(peptide)
peptideViewFrame <- gtkFrame('Information')
peptideTab$packStart(peptideViewFrame)
peptideViewScroll <- gtkScrolledWindow()
peptideViewScroll['border-width'] <- 5
peptideViewScroll$setPolicy(hscrollbar.policy=GtkPolicyType[2], vscrollbar.policy=GtkPolicyType[1])
peptideViewFrame$add(peptideViewScroll)
resultNotebook$appendPage(peptideTab, gtkLabel('Peptides'))
proteinTab <- gtkVBox(FALSE, 5)
proteinTab['border-width'] <- 5
proteinTopBox <- gtkHBox(FALSE, 5)
proteinTab$packStart(proteinTopBox)
proteinScroll <- gtkScrolledWindow()
proteinTopBox$packStart(proteinScroll)
protein <- gtkTreeView(proteins)
protein$insertColumnWithAttributes(position=-1, title='Protein', cell=gtkCellRendererText(), text=0)
proteinScroll$add(protein)
proteinSelect <- protein$getSelection()
gSignalConnect(protein, 'cursor-changed', f=function(...){
proteinName <- with(proteinSelect$getSelected(), model$getValue(iter, 0)$value)
proteinSequenceFromDB <- findProteinSequence(proteinName)
if(sampleFilter() == 'All'){
evidenceList <- findProteinEvidence(proteinName, FDR=FDR$getValue())
} else {
evidenceList <- findProteinEvidence(proteinName, sample=sampleFilter(), FDR=FDR$getValue())
}
evidenceLocation <- findProteinEvidenceLocation(proteinSequenceFromDB[[1]]$sequence, evidenceList, collate=FALSE)
tempPeptideSelection$unselectAll()
nPeptideValue$setText(length(evidenceList))
coverageValue$setText(paste(sprintf('%.1f', 100*length(unique(unlist(lapply(evidenceLocation, function(x) x[1]:x[2]))))/nchar(proteinSequenceFromDB[[1]]$sequence)), '%'))
protLengthValue$setText(nchar(proteinSequenceFromDB[[1]]$sequence))
protMassValue$setText(paste(sprintf('%.2f', pepMass(proteinSequenceFromDB[[1]]$sequence)), 'Da'))
protPIValue$setText(sprintf('%.2f', peppI(proteinSequenceFromDB[[1]]$sequence)))
hydroValue$setText(sprintf('%.1f', Qval(proteinSequenceFromDB[[1]]$sequence)))
tempPeptideList$setFrame(data.frame(Peptides=paste(sapply(evidenceLocation, '[', 1), '-', sapply(evidenceLocation, '[', 2), ': ', names(evidenceList), sep=''), stringsAsFactors=FALSE))
tempSampleList$setFrame(data.frame(Samples=unique(rawResults[rawResults[, 'Protein'] == proteinName, 'SpecFile']), stringsAsFactors=FALSE))
sequenceLabel$setMarkup(formatProteinPango(proteinSequenceFromDB[[1]]$sequence, evidenceList))
})
proteinTopBoxRight <- gtkVBox(FALSE, 5)
proteinTopBox$packStart(proteinTopBoxRight)
proteinPeptideScroll <- gtkScrolledWindow()
proteinTopBoxRight$packStart(proteinPeptideScroll)
tempPeptide <- gtkTreeView(tempPeptideList)
tempPeptide$insertColumnWithAttributes(position=-1, title='Peptide', cell=gtkCellRendererText(), text=0)
gSignalConnect(tempPeptide, 'cursor-changed', f=function(...){
proteinName <- with(proteinSelect$getSelected(), model$getValue(iter, 0)$value)
proteinSequenceFromDB <- findProteinSequence(proteinName)
if(sampleFilter() == 'All'){
evidenceList <- findProteinEvidence(proteinName, FDR=FDR$getValue())
} else {
evidenceList <- findProteinEvidence(proteinName, sample=sampleFilter(), FDR=FDR$getValue())
}
evidenceSelection <- as.numeric(with(tempPeptideSelection$getSelected(), model$getPath(iter))$toString())+1
sequenceLabel$setMarkup(formatProteinPango(proteinSequenceFromDB[[1]]$sequence, evidenceList, evidenceSelection))
})
gSignalConnect(tempPeptide, 'row-activated', function(...){
selectedSequence <- strsplit(with(tempPeptideSelection$getSelected(), model$getValue(iter, 0)$value), ' ')[[1]][2]
peptidePath <- gtkTreePathNewFromString(which(peptides[] == selectedSequence)-1)
resultNotebook$setCurrentPage(resultNotebook$pageNum(peptideTab))
peptideSelection$selectPath(peptidePath)
peptide$scrollToCell(peptidePath, use.align=TRUE, row.align=0.5)
gSignalEmit(peptide, 'cursor-changed')
})
tempPeptideSelection <- tempPeptide$getSelection()
proteinPeptideScroll$add(tempPeptide)
proteinSampleScroll <- gtkScrolledWindow()
proteinTopBoxRight$packStart(proteinSampleScroll)
tempSamples <- gtkTreeView(tempSampleList)
tempSamples$insertColumnWithAttributes(position=-1, title='Samples', cell=gtkCellRendererText(), text=0)
proteinSampleScroll$add(tempSamples)
proteinBottomBox <- gtkHBox(FALSE, 5)
proteinTab$packStart(proteinBottomBox, expand=FALSE, fill=FALSE)
proteinSequence <- gtkFrame('Sequence:')
proteinSequenceScroll <- gtkScrolledWindow()
proteinSequenceScroll['border-width'] <- 5
proteinSequenceScroll['vscrollbar-policy'] <- GtkPolicyType[1]
proteinSequenceScroll['hscrollbar-policy'] <- GtkPolicyType[3]
proteinSequence$add(proteinSequenceScroll)
sequenceLabel <- gtkLabel()
sequenceLabel['selectable'] <- TRUE
sequenceLabel$setLineWrap(TRUE)
sequenceLabel$setLineWrapMode('PANGO_WRAP_WORD')
font_descr <- pangoFontDescriptionNew()
font_descr$setFamily('courier')
sequenceLabel$modifyFont(font_descr)
proteinSequenceScroll$addWithViewport(sequenceLabel)
proteinSequenceScroll$getChild()$setShadowType(GtkShadowType[1])
proteinBottomBox$packStart(proteinSequence, expand=FALSE, fill=FALSE)
proteinInformationFrame <- gtkFrame('Information:')
proteinInformationTable <- gtkTable(rows=8, columns=2, homogeneous=FALSE)
proteinInformationTable['border-width'] <- 5
nPeptideLabel <- gtkLabel('Number of detected peptides:')
nPeptideLabel['xalign'] <- 1
proteinInformationTable$attach(nPeptideLabel, left.attach=0,1, top.attach=0,1)
nPeptideValue <- gtkLabel()
nPeptideValue['xalign'] <- 0
proteinInformationTable$attach(nPeptideValue, left.attach=1,2, top.attach=0,1)
coverageLabel <- gtkLabel('Coverage:')
coverageLabel['xalign'] <- 1
proteinInformationTable$attach(coverageLabel, left.attach=0,1, top.attach=1,2)
coverageValue <- gtkLabel()
coverageValue['xalign'] <- 0
proteinInformationTable$attach(coverageValue, left.attach=1,2, top.attach=1,2)
protLengthLabel <- gtkLabel('Length (residues):')
protLengthLabel['xalign'] <- 1
proteinInformationTable$attach(protLengthLabel, left.attach=0,1, top.attach=2,3)
protLengthValue <- gtkLabel()
protLengthValue['xalign'] <- 0
proteinInformationTable$attach(protLengthValue, left.attach=1,2, top.attach=2,3)
protMassLabel <- gtkLabel('Mass:')
protMassLabel['xalign'] <- 1
proteinInformationTable$attach(protMassLabel, left.attach=0,1, top.attach=3,4)
protMassValue <- gtkLabel()
protMassValue['xalign'] <- 0
proteinInformationTable$attach(protMassValue, left.attach=1,2, top.attach=3,4)
protPILabel <- gtkLabel('Isoelectric point (pI):')
protPILabel['xalign'] <- 1
proteinInformationTable$attach(protPILabel, left.attach=0,1, top.attach=4,5)
protPIValue <- gtkLabel()
protPIValue['xalign'] <- 0
proteinInformationTable$attach(protPIValue, left.attach=1,2, top.attach=4,5)
hydroLabel <- gtkLabel('Hydrophobicity (Q Value):')
hydroLabel['xalign'] <- 1
proteinInformationTable$attach(hydroLabel, left.attach=0,1, top.attach=5,6)
hydroValue <- gtkLabel()
hydroValue['xalign'] <- 0
proteinInformationTable$attach(hydroValue, left.attach=1,2, top.attach=5,6)
blastButton <- gtkButton('BLAST')
blastButton['width-request'] <- 80
blastButton['height-request'] <- 40
gSignalConnect(blastButton, 'clicked', f=function(...){
sequence <- findProteinSequence(with(proteinSelect$getSelected(), model$getValue(iter, 0)$value))
RID <- blastPut(sequence[[1]]$sequence, db='nr')
while(blastCheck(RID) != 'READY'){
Sys.sleep(5)
if(blastCheck(RID) != 'WAITING'){
stop('Unknown problem occured')
}
}
blastGet(RID)
})
proteinInformationTable$attach(blastButton, left.attach=0,2, top.attach=6,8, xoptions='', yoptions='')
proteinInformationTable$setRowSpacings(15)
proteinInformationTable$setColSpacings(5)
proteinInformationFrame$add(proteinInformationTable)
proteinBottomBox$packStart(proteinInformationFrame)
resultNotebook$appendPage(proteinTab, gtkLabel('Proteins'))
rawTab <- gtkVBox(FALSE, 5)
rawTab['border-width'] <- 5
rawExpander <- gtkExpander(label='Spectrum plot')
rawPlotAndSettingsBox <- gtkVBox(FALSE, 5)
rawExpander$add(rawPlotAndSettingsBox)
rawSettingsExpander <- gtkExpander(label='Settings')
rawSettingsExpander['border-width'] <- 5
rawSettingsBox <- gtkHBox(FALSE, 5)
rawSettingsBox$packStart(gtkHBox(), expand=TRUE, fill=TRUE)
rawSettingsTable <- gtkTable(rows=3, columns=7, homogeneous=FALSE)
rawSettingsTable$setColSpacing(0, 5)
rawSettingsTable$setColSpacing(1, 70)
rawSettingsTable$setColSpacing(2, 5)
ppmLabel <- gtkLabel('ppm: ')
ppmLabel['xalign'] <- 1
rawSettingsTable$attach(ppmLabel, left.attach=0,1, top.attach=0,1)
ppmPlotSetting <- gtkEntry()
ppmPlotSetting$setText('20')
ppmPlotSetting['height-request'] <- 24
ppmPlotSetting['width-request'] <- 40
gSignalConnect(ppmPlotSetting, 'activate', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(ppmPlotSetting, left.attach=1,2, top.attach=0,1)
neutralLabel <- gtkLabel('Neutral losses: ')
neutralLabel['xalign'] <- 1
rawSettingsTable$attach(neutralLabel, left.attach=0,1, top.attach=1,2)
neutralPlotSetting <- gtkCheckButton()
neutralPlotSetting$setActive(TRUE)
gSignalConnect(neutralPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(neutralPlotSetting, left.attach=1,2, top.attach=1,2)
traceLabel <- gtkLabel('Ion trace: ')
traceLabel['xalign'] <- 1
rawSettingsTable$attach(traceLabel, left.attach=0,1, top.attach=2,3)
tracePlotSetting <- gtkCheckButton()
tracePlotSetting$setActive(TRUE)
gSignalConnect(tracePlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(tracePlotSetting, left.attach=1,2, top.attach=2,3)
ionsLabel <- gtkLabel('Ions:')
ionsLabel['xalign'] <- 1
rawSettingsTable$attach(ionsLabel, left.attach=2,3, top.attach=0,1)
aIonLabel <- gtkLabel('a:')
aIonLabel['xalign'] <- 1
rawSettingsTable$attach(aIonLabel, left.attach=3,4, top.attach=0,1)
aIonPlotSetting <- gtkCheckButton()
aIonPlotSetting$setActive(TRUE)
gSignalConnect(aIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(aIonPlotSetting, left.attach=4,5, top.attach=0,1)
bIonLabel <- gtkLabel('b:')
bIonLabel['xalign'] <- 1
rawSettingsTable$attach(bIonLabel, left.attach=3,4, top.attach=1,2)
bIonPlotSetting <- gtkCheckButton()
bIonPlotSetting$setActive(TRUE)
gSignalConnect(bIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(bIonPlotSetting, left.attach=4,5, top.attach=1,2)
cIonLabel <- gtkLabel('c:')
cIonLabel['xalign'] <- 1
rawSettingsTable$attach(cIonLabel, left.attach=3,4, top.attach=2,3)
cIonPlotSetting <- gtkCheckButton()
gSignalConnect(cIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(cIonPlotSetting, left.attach=4,5, top.attach=2,3)
xIonLabel <- gtkLabel('x:')
xIonLabel['xalign'] <- 1
rawSettingsTable$attach(xIonLabel, left.attach=5,6, top.attach=0,1)
xIonPlotSetting <- gtkCheckButton()
gSignalConnect(xIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(xIonPlotSetting, left.attach=6,7, top.attach=0,1)
yIonLabel <- gtkLabel('y:')
yIonLabel['xalign'] <- 1
rawSettingsTable$attach(yIonLabel, left.attach=5,6, top.attach=1,2)
yIonPlotSetting <- gtkCheckButton()
yIonPlotSetting$setActive(TRUE)
gSignalConnect(yIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(yIonPlotSetting, left.attach=6,7, top.attach=1,2)
zIonLabel <- gtkLabel('z:')
zIonLabel['xalign'] <- 1
rawSettingsTable$attach(zIonLabel, left.attach=5,6, top.attach=2,3)
zIonPlotSetting <- gtkCheckButton()
gSignalConnect(zIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(zIonPlotSetting, left.attach=6,7, top.attach=2,3)
rawSettingsBox$packStart(rawSettingsTable)
rawSettingsBox$packStart(gtkHBox(), expand=TRUE, fill=TRUE)
rawSettingsExpander$add(rawSettingsBox)
rawPlotAndSettingsBox$packStart(rawSettingsExpander)
rawTab$packStart(rawExpander, expand=FALSE, fill=FALSE)
rawPlotBox <- gtkVBox(FALSE, 5)
rawPlotBox['height-request'] <- 400
rawPlotAndSettingsBox$packStart(rawPlotBox)
rawExpander$setExpanded(TRUE)
spectrumPlot <- gtkDrawingArea()
rawPlotBox$packStart(spectrumPlot)
rawScroll <- gtkScrolledWindow()
rawTab$packStart(rawScroll)
raw <- gtkTreeView(rawResultsFilter)
for(i in 1:(ncol(rawResults)-2)){
raw$insertColumnWithAttributes(position=-1, title=dimnames(rawResults)[[2]][i], cell=gtkCellRendererText(), text=i-1)
}
rawSelect <- raw$getSelection()
rawScroll$add(raw)
gSignalConnect(raw, 'row-activated', f=function(treeview, path, column, user.data){
model <- treeview$getModel()
selection <- model$getIter(path)$iter
sample <- treeview$getModel()$getValue(selection, 0)$value
if(!user.data$samples[user.data$samples[,'Samples']==sample, 'loaded']){
treeview$setData(key='msConnection', data=openMSfile(user.data$samples[user.data$samples[,'Samples']==sample, 'rawfile']))
user.data$samples[user.data$samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- model$getValue(selection, 2)$value
seq <- model$getValue(selection, 16)$value
user.data$expander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=treeview$getData('msConnection'), scan=scan, seq=seq, device=user.data$spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
treeview$scrollToCell(path)
}, data=list(samples=samples, expander=rawExpander, spectrumPlot=spectrumPlot))
gSignalConnect(rawSelect, 'changed', f=function(select, user.data){
if(rawExpander$getExpanded()){
selection <- select$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!user.data$samples[user.data$samples[,'Samples']==sample, 'loaded']){
user.data$raw$setData(key='msConnection', data=openMSfile(user.data$samples[user.data$samples[,'Samples']==sample, 'rawfile']))
user.data$samples[user.data$samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=user.data$raw$getData('msConnection'), scan=scan, seq=seq, device=user.data$spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
} else {}
}, data=list(samples=samples, raw=raw, spectrumPlot=spectrumPlot))
resultNotebook$appendPage(rawTab, gtkLabel('Raw data'))
statusbar <- gtkStatusbar()
topGroup$packStart(statusbar, expand=FALSE, fill=FALSE)
mainWindow$show()
asCairoDevice(FDRplot)
FDRplot$setData(key='Device', data=dev.cur())
grid.newpage()
#asCairoDevice(pepNumberPlot)
#pepNumberPlot$setData(key='Device', data=dev.cur())
resultNotebook$setCurrentPage(3)
asCairoDevice(spectrumPlot)
spectrumPlot$setData(key='Device', data=dev.cur())
grid.newpage()
resultNotebook$setCurrentPage(0)
rawExpander$setExpanded(FALSE)
thomasp85/pepmapsGUI documentation built on May 31, 2019, 11:15 a.m.
R Package Documentation
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# TODO: Add comment
#
# Author: Thomas
###############################################################################
library(pepmaps)
library(RGtk2)
library(ggplot2)
library(scales)
library(plyr)
library(cairoDevice)
library(grid)
library(mzR)
library(XML)
library(Biostrings)
filelist <- rGtkDataFrame(data.frame(Datafiles=character(), stringsAsFactors=FALSE))
gSignalConnect(filelist, 'row-inserted', f=function(treemodel, treepath, treeiter){
validButtons()
})
gSignalConnect(filelist, 'row-deleted', f=function(treemodel, treepath){
validButtons()
})
settingsSetNames <- c('New', 'Placeholder 1', 'Placeholder 2', 'Placeholder 3')
rawResults <- rGtkDataFrame(data.frame(SpecFile=character(), SpecID=character(), ScanNum=numeric(), FragMethod=character(), Precursor=numeric(), IsotopeError=numeric(), PrecursorError=numeric(), Charge=numeric(), Peptide=character(), Protein=character(), DeNovoScore=numeric(), MSGFScore=numeric(), SpecEValue=numeric(), EValue=numeric(), QValue=numeric(), PepQValue=numeric(), realPeptide=character(), '.vis'=logical(), stringsAsFactors=FALSE, check.names=FALSE))
#gSignalConnect(rawResults, 'row-inserted', f=function(treemodel, ...){
# resultBox$setSensitive(TRUE)
# peptides$setFrame(data.frame(Peptides=unique(rawResults[which(rawResults[,'.vis']), 'realPeptide'], stringsAsFactors=FALSE)))
# proteins$setFrame(data.frame(Proteins=unique(rawResults[which(rawResults[,'.vis']), 'Protein'], stringsAsFactors=FALSE)))
# })
#gSignalConnect(rawResults, 'row-deleted', f=function(treemodel, ...){
# if(nrow(rawResults[]) == 0){
# nPepID$setText('')
# nProtID$setText('')
# protIntersect$setText('')
# charge$setText(paste('', '\t(min)\n', '', '\t(median)\n', '', '\t(max)', sep=''))
# dev.set(FDRplot$getData('Device'))
# grid.newpage()
# dev.set(spectrumPlot$getData('Device'))
# grid.newpage()
# resultBox$setSensitive(FALSE)
# } else {
# peptides$setFrame(data.frame(Peptides=unique(rawResults[which(rawResults[,'.vis']), 'realPeptide'], stringsAsFactors=FALSE)))
# proteins$setFrame(data.frame(Proteins=unique(rawResults[which(rawResults[,'.vis']), 'Protein'], stringsAsFactors=FALSE)))
# sampleSelect$setActive(0)
# plotFDR(model=rawResults, sample='All', device=FDRplot$getData('Device'))
# }
# })
rawResultsFilter <- rawResults$filter()
rawResultsFilter$setVisibleColumn(ncol(rawResults)-1)
samples <- rGtkDataFrame(data.frame(Samples='All', '.notAll'=FALSE, loaded=FALSE, database=NA, rawfile=NA, resultfile=NA, check.names=FALSE, stringsAsFactors=FALSE))
gSignalConnect(samples, 'row-inserted', f=function(treemodel, treepath, treeiter, user.data){
nPepID$setText(length(peptides[]))
nProtID$setText(length(proteins[]))
protIntersect$setText(calcProtIntersect())
chargeSum <- summary(rawResults[rawResults[,'.vis'], 'Charge'])
charge$setText(paste(chargeSum['Min.'], '\t(min)\n', chargeSum['Median'], '\t(median)\n', chargeSum['Max.'], '\t(max)', sep=''))
})
samplesFilter <- samples$filter()
samplesFilter$setVisibleColumn(1)
peptides <- rGtkDataFrame(data.frame(Peptides=character(), stringsAsFactors=FALSE))
proteins <- rGtkDataFrame(data.frame(Proteins=character(), stringsAsFactors=FALSE))
tempPeptideList <- rGtkDataFrame(data.frame(Peptides=character(), stringsAsFactors=FALSE))
tempSampleList <- rGtkDataFrame(data.frame(Samples=character(), stringsAsFactors=FALSE))
collectSettings <- function(){
ans <- list()
ans$tolerance <- paste(sub(',', '.', toleranceValue$getText()), toleranceUnit$getActiveText(), sep='')
ans$isotopeError <- c(isotopeErrorLow$getValue(), isotopeErrorHigh$getValue())
ans$tda <- tdaToggle$getMode()
ans$fragmentation <- fragmentation$getActiveText()
ans$instrument <- instrument$getActiveText()
ans$protease <- enzyme$getActiveText()
ans$termini <- termini$getValue()
if(modification$getText() != 'Modification file...' & modification$getText() != ''){
if(file.exists(modification$getText())){
ans$modification <- modification$getText()
} else {
modificationWarning <- gtkMessageDialog(parent=mainWindow, flags='modal', type='warnings', buttons='ok', 'Modification file ignored', show=FALSE)
modificationWarning['title'] <- 'File problem'
gSignalConnect(modificationWarning, 'response', f=function(dialog, response, data){
dialog$destroy()
})
modificationWarning$show()
}
} else {}
ans$lengthRange <- c(lengthLow$getValue(), lengthHigh$getValue())
ans$chargeRange <- c(chargeLow$getValue(), chargeHigh$getValue())
ans$matches <- match$getValue()
ans
}
validButtons <- function(){
fileCheck <- nrow(filelist[drop=FALSE]) == 0
databaseCheck <- database$getText() == 'Database fasta file...' | database$getText() == ''
if(!databaseCheck){
databaseCheck <- !file.exists(database$getText())
} else {}
modificationCheck <- modification$getText() == 'Modification file...' | modification$getText() == ''
if(!modificationCheck){
modificationCheck <- !file.exists(modification$getText())
} else {
modificationCheck <- FALSE
}
if(fileCheck){
fileRemoveButton['sensitive'] <- FALSE
} else {
fileRemoveButton['sensitive'] <- TRUE
}
if(any(c(fileCheck, databaseCheck, modificationCheck))){
analyzeButton['sensitive'] <- FALSE
} else {
analyzeButton['sensitive'] <- TRUE
}
}
rawFilter <- function(data, sample, FDR, decoy=TRUE){
if(decoy){
ifelse(data[,1] == sample | sample == 'All', ifelse(data[,15] <= FDR, ifelse(!grepl('XXX_', data[,10]), TRUE, FALSE), FALSE), FALSE)
} else {
ifelse(data[,1] == sample | sample == 'All', ifelse(data[,15] <= FDR, TRUE, FALSE), FALSE)
}
}
sampleFilter <- function(){
ans <- sampleSelect$getActiveIter()
if(ans$retval){
ans <- samples$getValue(ans$iter, 0)$value
} else {
ans <- 'All'
}
ans
}
rawUpdated <- function(){
if(nrow(rawResults[]) == 0){
resultNotebook$setCurrentPage(resultNotebook$pageNum(summaryTab))
nPepID$setText('')
nProtID$setText('')
protIntersect$setText('')
charge$setText(paste('', '\t(min)\n', '', '\t(median)\n', '', '\t(max)', sep=''))
peptides$setFrame(data.frame(Peptides=character(), stringsAsFactors=FALSE))
proteins$setFrame(data.frame(Proteins=character(), stringsAsFactors=FALSE))
tempPeptideList$setFrame(data.frame(Peptides=character(), stringsAsFactors=FALSE))
tempSampleList$setFrame(data.frame(Samples=character(), stringsAsFactors=FALSE))
dev.set(FDRplot$getData('Device'))
grid.newpage()
dev.set(spectrumPlot$getData('Device'))
grid.newpage()
resultBox$setSensitive(FALSE)
} else {
resultBox$setSensitive(TRUE)
peptides$setFrame(data.frame(Peptides=unique(rawResults[which(rawResults[,'.vis']), 'realPeptide'], stringsAsFactors=FALSE)))
proteins$setFrame(data.frame(Proteins=unique(rawResults[which(rawResults[,'.vis']), 'Protein'], stringsAsFactors=FALSE)))
sampleSelect$setActive(0)
plotFDR(model=rawResults, sample='All', device=FDRplot$getData('Device'))
}
}
filterUpdated <- function(FDRChange=TRUE, SampleChange=TRUE){
if(length(samples[, 'Samples']) > 1){
rawResults[,'.vis'] <- rawFilter(rawResults[], sample=sampleFilter(), FDR=FDR$getValue())
peptides$setFrame(data.frame(Peptides=unique(rawResults[which(rawResults[,'.vis']), 'realPeptide'], stringsAsFactors=FALSE)))
proteins$setFrame(data.frame(Proteins=unique(rawResults[which(rawResults[,'.vis']), 'Protein'], stringsAsFactors=FALSE)))
#plotPepNumber(rawResults, sampleFilter(), FDR$getValue(), pepNumberPlot$getData('Device'))
nPepID$setText(length(peptides[]))
nProtID$setText(length(proteins[]))
chargeSum <- summary(rawResults[rawResults[,'.vis'], 'Charge'])
charge$setText(paste(chargeSum['Min.'], '\t(min)\n', chargeSum['Median'], '\t(median)\n', chargeSum['Max.'], '\t(max)', sep=''))
if(SampleChange){
plotFDR(rawResults, sampleFilter(), device=FDRplot$getData('Device'))
} else {}
if(FDRChange){
#FDR specific actions here
} else {}
} else {}
}
plotFDR <- function(model, sample, device){
if(sample == 'All'){
df <- model[]
} else {
df <- model[model[,'SpecFile'] == sample, ]
}
df$Score <- -log(df$SpecEValue)
df$decoy <- grepl('XXX_', df$Protein)
p <- ggplot(data=df, aes(x=Score, group=decoy, fill=decoy)) + theme_bw()
p <- p + geom_density(alpha=I(0.5)) + scale_fill_manual('', breaks=c(FALSE, TRUE), labels=c('Database ', 'Decoy'), values=c('#468966', '#B64926'))
p <- p + scale_x_continuous(limits=c(0, max(df$Score)), expand=c(0,0)) + scale_y_continuous(expand=c(0,0))
p <- p + theme(panel.border=element_blank(), panel.grid=element_blank(), axis.line=element_line(size=0.5), legend.position='bottom')
dev.set(device)
print(p)
}
plotPepNumber <- function(model, sample, FDR, device){
if(sample == 'All'){
df <- model[model[,'QValue'] <= FDR,]
} else {
df <- model[model[,'SpecFile'] == sample & model[,'QValue'] <= FDR, ]
}
df <- df[!grepl('XXX_', df$Protein),]
nPep <- daply(df, .(Protein), function(x) length(unique(x$realPeptide)))
p <- ggplot(data=data.frame(nPep=nPep)) + geom_histogram(aes(x=nPep)) + coord_flip() + scale_x_reverse()
p <- p + theme_bw() + theme(panel.border=element_blank(), panel.grid=element_blank(), axis.line=element_line(size=0.5))
dev.set(device)
print(p)
}
calcProtIntersect <- function(){
df <- rawResults[]
df <- df[!grepl('XXX_', df$Protein),]
df <- df[df$QValue <= FDR$getValue(), ]
names(df)[1] <- sub('#', '', names(df)[1])
df <- dlply(df, .(SpecFile), function(x) unique(x$Protein))
length(Reduce(intersect, df))
}
traceIon <- function(data, index, mz, ppm){
indexRange <- c(1, length(data))
mzWin <- c(mz-(mz/1000000)*ppm, mz+(mz/1000000)*ppm)
scan <- peaks(data, index)
mzIndex <- which(scan[,1] > mzWin[1] & scan[,1] < mzWin[2])
if(length(mzIndex) == 0){
intensity <- c()
retention <- c()
} else {
if(length(mzIndex) != 1){
mzIndex <- mzIndex[which.max(scan[mzIndex, 2])]
} else {}
intensity <- c(scan[mzIndex, 2])
retention <- c(header(data, index)$retentionTime)
}
indexBack <- index
indexForward <- index
doBreak <- FALSE
nextIter <- 1
while(as.logical(nextIter)){
indexBack <- indexBack-1
while(header(data, indexBack)$msLevel == 2){
indexBack <- indexBack-1
if(indexBack <= indexRange[1]){
doBreak <- TRUE
break
}
}
if(doBreak) break
if(indexBack < 1) break
scan <- peaks(data, indexBack)
mzIndex <- which(scan[,1] > mzWin[1] & scan[,1] < mzWin[2])
if(length(mzIndex) == 0){
nextIter <- nextIter + 1
} else {
if(length(mzIndex) != 1){
mzIndex <- mzIndex[which.max(scan[mzIndex, 2])]
} else {}
intensity <- c(scan[mzIndex, 2], intensity)
retention <- c(header(data, indexBack)$retentionTime, retention)
}
if(nextIter > 2){
nextIter <- 0
}
if(indexBack <= indexRange[1]){
nextIter <- 0
}
}
nextIter <- 1
doBreak <- FALSE
while(as.logical(nextIter)){
indexForward <- indexForward+1
while(header(data, indexForward)$msLevel == 2){
indexForward <- indexForward+1
if(indexForward >= indexRange[2]){
doBreak <- TRUE
break
}
}
if(doBreak) break
scan <- peaks(data, indexForward)
mzIndex <- which(scan[,1] > mzWin[1] & scan[,1] < mzWin[2])
if(length(mzIndex) == 0){
nextIter <- nextIter + 1
} else {
if(length(mzIndex) != 1){
mzIndex <- mzIndex[which.max(scan[mzIndex, 2])]
} else {}
intensity <- c(intensity, scan[mzIndex, 2])
retention <- c(retention, header(data, indexForward)$retentionTime)
}
if(nextIter > 2){
nextIter <- 0
}
if(indexForward >= indexRange[2]){
nextIter <- 0
}
}
data.frame(intensity, retention)
}
plotSpectrum <- function(data, scan, seq, ppm=40, device, ionTrace=TRUE, ions='aby', neutralLosses=TRUE){
if(missing(device)){
device <- dev.cur()
}
index <- which(header(data)$acquisitionNum == scan)
scanInfo <- header(data, index)
spec <- peaks(data, index)
spec <- data.frame(mz=spec[,1], intensity=spec[,2], ymin=0)
if(scanInfo$msLevel > 1){
precursor <- which.min(abs(spec$mz-scanInfo$precursorMZ))
if(abs(spec$mz[precursor]-scanInfo$precursorMZ) < (scanInfo$precursorMZ/1000000)*ppm){
precursor <- spec[precursor, , drop=FALSE]
} else {
precursor <- data.frame()
}
} else {
precursor <- data.frame()
}
if(!missing(seq)){
p <- ggplot() + geom_linerange(data=spec, aes(x=mz, ymax=intensity, ymin=ymin), colour=I('grey'))
if(nrow(precursor) != 0){
p <- p + geom_point(data=precursor, aes(x=mz, y=intensity), size=I(3), colour=I('#B64926'))
}
ionlab <- data.frame(spec, ion=NA)
ionlist <- pepmaps:::fragPattern(seq, ions=ions, neutralLosses=neutralLosses)
for(i in 1:nrow(ionlist)){
ind <- which(ionlab$mz < ionlist$mz[i]+(ionlist$mz[i]/1000000)*ppm & ionlab$mz > ionlist$mz[i]-(ionlist$mz[i]/1000000)*ppm)
if(length(ind) == 1){
ionlab$ion[ind] <- ionlist$ion[i]
} else if(length(ind) > 1){
ind <- ind[which.min(abs(ionlab$mz[ind]-ionlist$mz[i]))]
ionlab$ion[ind] <- ionlist$ion[i]
} else {}
}
ionlab <- ionlab[!is.na(ionlab$ion),]
if(nrow(ionlab) != 0){
p <- p + geom_linerange(data=ionlab, aes(x=mz, ymax=intensity, ymin=ymin))
p <- p + geom_text(data=ionlab, aes(x=mz, y=intensity, label=ion), colour=I('#468966'), vjust=-0.5, size=4)
} else {}
} else {}
p <- p + theme_bw() + theme(panel.border=element_blank(), panel.grid=element_blank(), axis.line=element_line(size=0.5), legend.position='bottom')
p <- p + scale_y_continuous('Intensity', expand=c(0,0), limits=c(0, max(spec$intensity)*1.1))
if(ionTrace){
parentIndex <- which(header(data)$acquisitionNum == scanInfo$precursorScanNum)
parentInfo <- header(data, parentIndex)
intensity <- peaks(data, parentIndex)
parentData <- data.frame(retention=parentInfo$retentionTime, intensity=intensity[which.min(abs(intensity[, 1]-scanInfo$precursorMZ)), 2])
trace <- traceIon(data, parentIndex, scanInfo$precursorMZ, ppm)
parentLines <- data.frame(x=c(min(trace$retention), parentData$retention), xend=c(parentData$retention, parentData$retention), y=c(parentData$intensity, min(trace$intensity)), yend=c(parentData$intensity, parentData$intensity))
q <- ggplot(data=trace, aes(x=retention, y=intensity)) + geom_line()
q <- q + geom_segment(data=parentLines, aes(x=x, xend=xend, y=y, yend=yend), linetype=I(2))
q <- q + geom_point(data=parentData, size=I(3), colour=I('#B64926'))
q <- q + theme_minimal() + theme(panel.grid=element_blank(), axis.ticks=element_blank(), plot.background=element_rect(colour=alpha('#F5F5F5', 0.75), fill=alpha('#F5F5F5', 0.75)), plot.margin=unit(c(10, 10, 0, 0), 'points'))
q <- q + scale_y_continuous('', expand=c(0,0), breaks=parentData$intensity) + scale_x_continuous('', expand=c(0,0), breaks=parentData$retention)
} else {}
dev.set(device)
print(p)
if(ionTrace){
vp <- viewport(width=0.4, height=0.3, x=0.98, y=0.98, just=c('right', 'top'))
print(q, vp=vp)
}
}
collectRawPlotSettings <- function(){
ans <- list()
ans$ppm <- as.numeric(ppmPlotSetting$getText())
ans$neutralLosses <- neutralPlotSetting$getActive()
ans$ionTrace <- tracePlotSetting$getActive()
ans$ions <- paste(if(aIonPlotSetting$getActive()) 'a', if(bIonPlotSetting$getActive()) 'b', if(cIonPlotSetting$getActive()) 'c', if(xIonPlotSetting$getActive()) 'x', if(yIonPlotSetting$getActive()) 'y', if(zIonPlotSetting$getActive()) 'z', sep='')
ans
}
getRunInfoFromMZID <- function(file){
parsedMZID <- xmlTreeParse(file, useInternalNodes=TRUE)
rootMZID <- xmlRoot(parsedMZID)
database <- xmlAttrs(rootMZID[['DataCollection']][['Inputs']][['SearchDatabase']])['location']
if(!file.exists(database)){
database <- file.path(dirname(file), basename(database))
if(!file.exists(database)){
database <- NA
} else {}
} else {}
rawfile <- xmlAttrs(rootMZID[['DataCollection']][['Inputs']][['SpectraData']])['location']
if(!file.exists(rawfile)){
rawfile <- file.path(dirname(file), basename(rawfile))
if(!file.exists(rawfile)){
rawfile <- NA
} else {}
} else {}
resultfile <- file
analysisPar <- list()
for(i in 1:length(xmlSApply(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['AdditionalSearchParams']], xmlName))){
if(xmlName(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['AdditionalSearchParams']][[i]]) == 'userParam'){
param <- xmlAttrs(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['AdditionalSearchParams']][[i]])
if(param['name'] == 'TargetDecoyApproach'){
analysisPar$tda <- as.logical(param['value'])
} else if(param['name'] == 'MinIsotopeError'){
analysisPar$isotopeError[1] <- as.numeric(param['value'])
} else if(param['name'] == 'MaxIsotopeError'){
analysisPar$isotopeError[2] <- as.numeric(param['value'])
} else if(param['name'] == 'FragmentMethod'){
analysisPar$fragmentation <- param['value']
} else if(param['name'] == 'Instrument'){
analysisPar$instrument <- param['value']
} else if(param['name'] == 'NumTolerableTermini'){
analysisPar$termini <- as.numeric(param['value'])
} else if(param['name'] == 'NumMatchesPerSpec'){
analysisPar$matches <- as.numeric(param['value'])
} else if(param['name'] == 'MinPepLength'){
analysisPar$lengthRange[1] <- as.numeric(param['value'])
} else if(param['name'] == 'MaxPepLength'){
analysisPar$lengthRange[2] <- as.numeric(param['value'])
} else if(param['name'] == 'MinCharge'){
analysisPar$chargeRange[1] <- as.numeric(param['value'])
} else if(param['name'] == 'MaxCharge'){
analysisPar$chargeRange[2] <- as.numeric(param['value'])
} else {}
} else {}
}
analysisPar$protease <- xmlAttrs(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['Enzymes']][['Enzyme']][['EnzymeName']][['cvParam']])['name']
analysisPar$tolerance <- as.numeric(xmlAttrs(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['ParentTolerance']][['cvParam']])['value'])
tolUnit <- xmlAttrs(rootMZID[['AnalysisProtocolCollection']][['SpectrumIdentificationProtocol']][['ParentTolerance']][['cvParam']])['unitName']
if(tolower(tolUnit) == 'parts per million'){
analysisPar$tolerance <- paste(analysisPar$tolerance, 'ppm', sep='')
} else if(tolower(tolUnit) == 'dalton'){
analysisPar$tolerance <- paste(analysisPar$tolerance, 'Da', sep='')
} else {
analysisPar$tolerance <- as.character(analysisPar$tolerance)
}
free(parsedMZID)
list(database=database, rawfile=rawfile, resultfile=resultfile, parameters=analysisPar)
}
updateSampleList <- function(add){
newSample <- data.frame(Samples=basename(add$rawfile), '.notAll'=TRUE, loaded=FALSE, database=add$database, rawfile=add$rawfile, resultfile=add$resultfile, check.names=FALSE, stringsAsFactors=FALSE)
if(any(samples[,'Samples'] %in% newSample$Samples)){
} else {}
samples$appendRows(newSample)
}
findProteinSequence <- function(name){
rawfiles <- unique(as.character(rawResults[rawResults[,'Protein'] == name, 1]))
databases <- unique(samples[samples[, 'Samples'] %in% rawfiles, 'database'])
seq <- list()
for(i in 1:length(databases)){
seqs <- readAAStringSet(databases[i])
ans <- list(sequence=as.character(seqs[which(sapply(strsplit(names(seqs), ' '), '[', 1) == name)]), files=samples[which(samples[, 'database'] == databases[i]), 'Samples'])
seq[[i]] <- ans
}
seq
}
findProteinEvidence <- function(name, sample, FDR){
if(missing(sample)){
ind <- which(rawResults[, 'Protein'] == name & rawResults[, 'QValue'] <= FDR)
ans <- rawResults[ind, 'realPeptide']
} else {
ind <- which(rawResults[, 'Protein'] == name & rawResults[, 'SpecFile'] == sample & rawResults[, 'QValue'] <= FDR)
ans <- rawResults[ind, 'realPeptide']
}
split(ind, ans)
}
findProteinEvidenceLocation <- function(sequence, evidence, collate=TRUE){
ans <- list()
for(i in 1:length(evidence)){
m <- regexpr(names(evidence)[i], sequence)
ans[[i]] <- c(m, m+attr(m, 'match.length')-1)
}
if(collate){
m <- sort(unique(unlist(lapply(ans, function(x) seq(x[1], x[2])))))
d <- diff(m)
d1 <- which(d != 1)
ans <- list()
if(length(d1) == 0){
ans[[1]] <- c(m[1], m[length(m)])
} else {
ans[[1]] <- c(m[1], m[d1[1]])
if(length(d1) > 1){
for(i in 2:length(d1)){
ans[[i]] <- c(m[d1[i-1]+1], m[d1[i]])
}
}
ans[[length(ans)+1]] <- c(m[d1[length(d1)]+1], m[length(m)])
}
} else {}
ans
}
formatProteinPango <- function(sequence, evidence, evidenceHighlight, breakPosition=40){
markupLocation <- findProteinEvidenceLocation(sequence, evidence, collate=TRUE)
if(!missing(evidenceHighlight)){
highlightLocation <- findProteinEvidenceLocation(sequence, evidence[evidenceHighlight], collate=FALSE)
}
sequence <- strsplit(sequence, '')[[1]]
ans <- c()
if(markupLocation[[1]][1] != 1){
ans <- paste(sequence[1:(markupLocation[[1]][1]-1)], collapse='')
} else {
ans <- c()
}
for(i in 1:length(markupLocation)){
if(!missing(evidenceHighlight) && markupLocation[[i]][1] <= highlightLocation[[1]][1] && markupLocation[[i]][2] >= highlightLocation[[1]][2]){
if(markupLocation[[i]][1] != highlightLocation[[1]][1]) ans <- paste(ans, '<span color=\'#B64926\'>', paste(sequence[markupLocation[[i]][1]:(highlightLocation[[1]][1]-1)], collapse=''), '</span>', sep='')
ans <- paste(ans, '<span bgcolor=\'#468966\'>', paste(sequence[highlightLocation[[1]][1]:highlightLocation[[1]][2]], collapse=''), '</span>', sep='')
if(markupLocation[[i]][2] != highlightLocation[[1]][2]) ans <- paste(ans, '<span color=\'#B64926\'>', paste(sequence[(highlightLocation[[1]][2]+1):markupLocation[[i]][2]], collapse=''), '</span>', sep='')
} else {
ans <- paste(ans, '<span color=\'#B64926\'>', paste(sequence[markupLocation[[i]][1]:markupLocation[[i]][2]], collapse=''), '</span>', sep='')
}
if(i != length(markupLocation)){
ans <- paste(ans, paste(sequence[(markupLocation[[i]][2]+1):(markupLocation[[i+1]][1]-1)], collapse=''), sep='')
}
}
if(markupLocation[[length(markupLocation)]][2] < length(sequence)){
ans <- paste(ans, paste(sequence[(markupLocation[[length(markupLocation)]][2]+1):length(sequence)], collapse=''), sep='')
}
if(breakPosition > 0 & breakPosition < length(sequence)){
seqSplitted <- regmatches(ans, gregexpr('<.*?>', ans, perl=T), invert=TRUE)
if(length(which(seqSplitted[[1]] == '') != 0)) {
addEmpty <- which(seqSplitted[[1]] == '')
seqSplitted[[1]] <- seqSplitted[[1]][-which(seqSplitted[[1]] == '')]
} else {
addEmpty <- c()
}
splitPosition <- split(rep(1:ceiling(length(sequence)/breakPosition), each=breakPosition)[1:length(sequence)], rep(1:length(seqSplitted[[1]]), nchar(seqSplitted[[1]])))
lineBreakInsert <- mapply(function(x, y) paste(unlist(sapply(split(x, y), function(x) c(x, '\n'))), collapse=''), strsplit(seqSplitted[[1]], ''), splitPosition)
for(i in 1:(length(lineBreakInsert)-1)){
if(splitPosition[[i]][length(splitPosition[[i]])] == splitPosition[[i+1]][1]){
lineBreakInsert[[i]] <- sub('\n$', '', lineBreakInsert[[i]], perl=T)
} else {}
}
lineBreakInsert[[length(lineBreakInsert)]] <- sub('\n$', '', lineBreakInsert[[length(lineBreakInsert)]], perl=T)
if(length(addEmpty) > 0){
for(i in addEmpty){
lineBreakInsert <- append(lineBreakInsert, '', i-1)
}
}
lineBreakInsert <- list(lineBreakInsert)
regmatches(ans, gregexpr('<.*?>', ans, perl=T), invert=TRUE) <- lineBreakInsert
}
ans
}
blastPut <- function(seq, db, ...){
### Based on blast.pdb
urlput <- paste("http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Put&DATABASE=", db,"&PROGRAM=blastp&CLIENT=web&QUERY=", seq, sep="")
txt <- scan(urlput, what="raw", sep="\n", quiet=TRUE)
rid <- sub("^.*RID = " ,"",txt[ grep("RID =",txt) ])
rid
}
blastCheck <- function(rid){
urlget <- paste("http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=",rid, sep="")
txt <- scan(urlget, what="raw", sep="\n", quiet=TRUE)
status <- sub("^.*Status=" ,"",txt[ grep("Status=",txt) ])
status
}
blastGet <- function(rid, browser=TRUE, ...){
urlget <- paste("http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=",rid, sep="")
if(browser){
browseURL(urlget)
}
}
formatPeptideSequence <- function(seq){
ans <- strsplit(seq, '.', fixed=T)[[1]]
ans <- paste(sub('-', '|', ans), collapse='--')
modPos <- c()
mod <- c()
while(1){
mods <- regexpr('\\+([\\d]|,)+', ans, perl=TRUE)
if(mods == -1){
break
} else {
modPos <- c(modPos, mods-1)
mod <- c(mod, regmatches(ans, mods))
regmatches(ans, mods) <- ''
}
}
top <- list(rep(' ', nchar(ans)), rep(' ', nchar(ans)))
bottom <- list(rep(' ', nchar(ans)), rep(' ', nchar(ans)))
if(length(modPos) > 0){
mod <- sub('+', '', mod, fixed=TRUE)
mod <- sub(',', '.', mod, fixed=TRUE)
for(i in length(modPos):1){
start <- 2
while(1){
if(start > length(top)){
top <- c(top, list(rep(' ', nchar(ans))))
} else {}
if(start > length(bottom)){
bottom <- c(bottom, list(rep(' ', nchar(ans))))
} else {}
if(all(top[[start]][modPos[i]:(modPos[i]+nchar(mod[i])-1)] == ' ', na.rm=TRUE)){
top[[start]][modPos[i]:(modPos[i]+nchar(mod[i])-1)] <- strsplit(mod, '')[[1]]
retract <- start-1
while(retract){
top[[retract]][modPos[i]] <- '|'
retract <- retract-1
}
break
} else if(all(bottom[[start]][modPos[i]:(modPos[i]+nchar(mod[i])-1)] == ' ', na.rm=TRUE)){
bottom[[start]][modPos[i]:(modPos[i]+nchar(mod[i])-1)] <- strsplit(mod, '')[[1]]
retract <- start-1
while(retract){
bottom[[retract]][modPos[i]] <- '|'
retract <- retract-1
}
break
} else {
start <- start+1
}
}
}
} else {}
top <- paste(sapply(top, paste, collapse=''), '\n', sep='')
bottom <- paste(sapply(bottom, paste, collapse=''), '\n', sep='')
ans <- c(rev(top), paste(ans, '\n', sep=''), bottom)
ans
}
createPeptideView <- function(seq){
VBox <- gtkVBox(FALSE, 5)
VBox['border-width'] <- 5
alternativeRawSeq <- unique(rawResults[rawResults[,'realPeptide'] == seq & rawResults[,'.vis'], 'Peptide'])
for(i in alternativeRawSeq){
if(i != alternativeRawSeq[1]){
separator <- gtkHSeparatorNew()
separator['height-request'] <- 30
VBox$packStart(separator, expand=FALSE, fill=FALSE)
}
peptideOverview <- gtkLabel(paste(formatPeptideSequence(i), collapse=''))
font_descr <- pangoFontDescriptionNew()
font_descr$setFamily('courier')
peptideOverview$modifyFont(font_descr)
peptideOverviewScroll <- gtkScrolledWindow()
peptideOverviewScroll$setPolicy(hscrollbar.policy=GtkPolicyType[2], vscrollbar.policy=GtkPolicyType[3])
peptideOverviewScroll$addWithViewport(peptideOverview)
peptideOverviewScroll$getChild()$setShadowType(GtkShadowType[1])
VBox$packStart(peptideOverviewScroll, expand=FALSE, fill=FALSE)
peptideViewTable <- gtkTable()
peptideViewTable['border-width'] <- 5
nDetectionLabel <- gtkLabel('Number of times detected:')
nDetectionLabel['xalign'] <- 1
peptideViewTable$attach(nDetectionLabel, left.attach=0,1, top.attach=0,1)
nDetectionValue <- gtkLabel(sum(rawResults[,'Peptide'] == i & rawResults[,'.vis']))
nDetectionValue['xalign'] <- 0
peptideViewTable$attach(nDetectionValue, left.attach=1,2, top.attach=0,1)
pepLengthLabel <- gtkLabel('Length (residues):')
pepLengthLabel['xalign'] <- 1
peptideViewTable$attach(pepLengthLabel, left.attach=0,1, top.attach=1,2)
pepLengthValue <- gtkLabel(nchar(seq))
pepLengthValue['xalign'] <- 0
peptideViewTable$attach(pepLengthValue, left.attach=1,2, top.attach=1,2)
pepMassLabel <- gtkLabel('Mass:')
pepMassLabel['xalign'] <- 1
peptideViewTable$attach(pepMassLabel, left.attach=0,1, top.attach=2,3)
pepMassValue <- gtkLabel(paste(sprintf('%.2f', pepMass(seq)), 'Da'))
pepMassValue['xalign'] <- 0
peptideViewTable$attach(pepMassValue, left.attach=1,2, top.attach=2,3)
pepPILabel <- gtkLabel('Isoelectric point (pI):')
pepPILabel['xalign'] <- 1
peptideViewTable$attach(pepPILabel, left.attach=0,1, top.attach=3,4)
pepPIValue <- gtkLabel(sprintf('%.2f', peppI(seq)))
pepPIValue['xalign'] <- 0
peptideViewTable$attach(pepPIValue, left.attach=1,2, top.attach=3,4)
hydroPepLabel <- gtkLabel('Hydrophobicity (Q Value):')
hydroPepLabel['xalign'] <- 1
peptideViewTable$attach(hydroPepLabel, left.attach=0,1, top.attach=4,5)
hydroPepValue <- gtkLabel(sprintf('%.1f', Qval(seq)))
hydroPepValue['xalign'] <- 0
peptideViewTable$attach(hydroPepValue, left.attach=1,2, top.attach=4,5)
peptideViewTable$setRowSpacings(15)
peptideViewTable$setColSpacings(5)
VBox$packStart(peptideViewTable, expand=FALSE, fill=FALSE)
peptideDF <- rawResults[rawResults[,'Peptide'] == i & rawResults[,'.vis'], ]
peptideViewModel <- gtkTreeStore('gchararray', 'gchararray', 'gchararray')
by(peptideDF, peptideDF$Protein, function(x){
parent_iter <- peptideViewModel$append()
peptideViewModel$setValue(parent_iter$iter, column=0, paste('Protein: ', x$Protein[1], sep=''))
by(x, x$SpecFile, function(y){
parent2_iter <- peptideViewModel$append(parent=parent_iter$iter)
peptideViewModel$setValue(parent2_iter$iter, column=0, paste('Sample: ', y$SpecFile[1], sep=''))
by(y, y$Charge, function(z){
parent3_iter <- peptideViewModel$append(parent=parent2_iter$iter)
peptideViewModel$setValue(parent3_iter$iter, column=0, paste('Charge: ', z$Charge[1], sep=''))
for(i in 1:nrow(z)){
child_iter <- peptideViewModel$append(parent=parent3_iter$iter)
peptideViewModel$setValue(child_iter$iter, column=1, value=z[i, 'ScanNum'])
peptideViewModel$setValue(child_iter$iter, column=2, value=z[i, 'QValue'])
}
})
})
})
peptideTreeView <- gtkTreeView()
peptideTreeView$insertColumnWithAttributes(-1, '', gtkCellRendererText(), text=0)
peptideTreeView$insertColumnWithAttributes(-1, 'Scan Number', gtkCellRendererText(), text=1)
peptideTreeView$insertColumnWithAttributes(-1, 'FDR', gtkCellRendererText(), text=2)
peptideTreeView$setModel(peptideViewModel)
peptideTreeViewScroll <- gtkScrolledWindow()
peptideTreeView['height-request'] <- 200
peptideTreeViewScroll$add(peptideTreeView)
peptideTreeSelection <- peptideTreeView$getSelection()
gSignalConnect(peptideTreeView, 'row-activated', function(...){
if(!with(peptideTreeSelection$getSelected(), model$iterParent(iter)$retval)){
proteinName <- with(peptideTreeSelection$getSelected(), model$getValue(iter, 0)$value)
proteinName <- sub('Protein: ', '', proteinName)
proteinPath <- gtkTreePathNewFromString(which(proteins[] == proteinName)-1)
resultNotebook$setCurrentPage(resultNotebook$pageNum(proteinTab))
proteinSelect$selectPath(proteinPath)
protein$scrollToCell(proteinPath, use.align=TRUE, row.align=0.5)
gSignalEmit(protein, 'cursor-changed')
} else if(!with(peptideTreeSelection$getSelected(), model$iterHasChild(iter))){
scanNum <- with(peptideTreeSelection$getSelected(), model$getValue(iter, 1)$value)
sample <- sub('Sample: ', '', with(peptideTreeSelection$getSelected(), with(model$iterParent(model$iterParent(iter)$iter), model$getValue(iter, 0)$value)))
proteinName <- sub('Protein: ', '', with(peptideTreeSelection$getSelected(), with(model$iterParent(model$iterParent(model$iterParent(iter)$iter)$iter), model$getValue(iter, 0)$value)))
ind <- which(rawResults[,'SpecFile'] == sample & rawResults[,'ScanNum'] == scanNum & rawResults[,'Protein'] == proteinName)
if(length(ind) == 1){
rawPath <- gtkTreePathNewFromString(ind-1)
resultNotebook$setCurrentPage(resultNotebook$pageNum(rawTab))
rawSelect$selectPath(rawPath)
raw$scrollToCell(rawPath)
raw$rowActivated(rawPath, gtkTreeViewColumn())
}
}
})
VBox$packStart(peptideTreeViewScroll, expand=FALSE, fill=FALSE)
}
viewportVBox <- gtkViewport()
viewportVBox$add(VBox)
viewportVBox$setShadowType(GtkShadowType[1])
return(viewportVBox)
}
mainWindow <- gtkWindow(show=FALSE)
mainWindow$setTitle('MS GF+')
topGroup <- gtkVBox(FALSE, 5)
mainWindow$add(topGroup)
toolbar <- gtkToolbar()
topGroup$packStart(toolbar, expand=FALSE)
importAction <- gtkAction(name='import', label='Import', tooltip='Import mzIdentML files', stock.id='gtk-add')
gSignalConnect(importAction, 'activate', f=function(...){
file <- gtkFileChooserDialog(title='Select MS datafiles', parent=NULL, action='open', 'gtk-ok', GtkResponseType['ok'], 'gtk-cancel', GtkResponseType['cancel'], show=FALSE)
file['select-multiple'] <- TRUE
gSignalConnect(file, 'response', f=function(dialog, response, data){
dialog$hide()
})
response <- file$Run()
if(response == GtkResponseType["ok"]){
filenames <- unlist(file$getFilenames())
for(i in 1:length(filenames)){
if(Sys.info()["sysname"] == 'Windows'){
filename <- paste('\"', filenames[i], '\"', sep='')
} else {
filename <- gsub(' ', '\\ ', filenames[i], fixed=T)
}
callConv <- paste('java -Xmx', 10000, 'M -cp ', R.home(component='library/pepmaps/java/MSGFplus.jar'), ' edu.ucsd.msjava.ui.MzIDToTsv -i ', filename, ' -o ', paste(filename, '.tsv', sep=''), ' -unroll 1 -showDecoy 1', sep='')
system(callConv)
if(length(scan(paste(filenames[i], '.tsv', sep=''), skip=1, nlines=1, what='character', quiet=T)) != 0){
results <- read.table(paste(filenames[i], '.tsv', sep=''), sep='\t', header=TRUE, comment.char='', stringsAsFactors=FALSE)
names(results) <- sub('#', '', scan(paste(filenames[i], '.tsv', sep=''), nlines=1, what=character(), quiet=TRUE))
unlink(paste(filenames[i], '.tsv', sep=''))
sNum <- regexpr('scanId=[\\d]+', results$SpecID, perl=TRUE)
sNum <- substr(results$SpecID, sNum, sNum+attr(sNum, 'match.length')-1)
sNum <- sub('scanId=', '', sNum)
results$ScanNum <- sNum
peptide <- strsplit(as.character(results$Peptide), '\\.')
peptide <- unlist(peptide)[seq(2, length(peptide)*3, by=3)]
peptide <- gsub('\\+([\\d]|,)+', '', peptide, perl=TRUE)
results$realPeptide <- peptide
results$'.vis' <- rawFilter(results, sample=sampleFilter(), FDR=FDR$getValue())
rawResults$appendRows(results)
rawUpdated()
sampleInfo <- getRunInfoFromMZID(filenames[i])
updateSampleList(add=sampleInfo)
} else {}
}
} else {}
file$destroy()
})
importToolButton <- importAction$createToolItem()
toolbar$add(importToolButton)
removeAction <- gtkAction(name='remove', label='Remove', tooltip='Remove analysis results', stock.id='gtk-remove')
gSignalConnect(removeAction, 'activate', f=function(...){
removeDialog <- gtkDialogNewWithButtons(title='Remove sample results', parent=mainWindow, flags=1, 'Remove', GtkResponseType['ok'], 'Cancel', GtkResponseType['cancel'], show=FALSE)
removeDialogContent <- removeDialog$getContentArea()
removeDialogScroll <- gtkScrolledWindow()
removeDialogContent$packStart(removeDialogScroll)
removeDialogList <- gtkTreeView(samplesFilter)
removeDialogList$insertColumnWithAttributes(position=-1, title='MS datafiles', cell=gtkCellRendererText(), text=0)
removeDialogList$setHeadersVisible(FALSE)
removeDialogList['height-request'] <- 100
removeDialogSelect <- removeDialogList$getSelection()
removeDialogSelect$setMode('multiple')
removeDialogScroll$add(removeDialogList)
gSignalConnect(removeDialog, 'response', f=function(dialog, response, ...){
if(response == GtkResponseType['ok']){
samplesToRemoveIndex <- sapply(removeDialogSelect$getSelectedRows()$retval, function(x) as.numeric(samplesFilter$convertPathToChildPath(x)$toString())+1)
samplesToRemove <- samples[samplesToRemoveIndex, 1]
allIndex <- which(samplesToRemove == 'All')
if(length(allIndex) != 0){
samplesToRemoveIndex <- samplesToRemoveIndex[-allIndex]
samplesToRemove <- samplesToRemove[-allIndex]
}
rawRowsToRemove <- which(rawResults[,'SpecFile'] %in% samplesToRemove)
samples$setFrame(data.frame(samples[-samplesToRemoveIndex, , drop=FALSE]))
rawResults$setFrame(data.frame(rawResults[-rawRowsToRemove, , drop=FALSE]))
rawUpdated()
}
dialog$Destroy()
})
removeDialog$show()
})
removeToolButton <- removeAction$createToolItem()
toolbar$add(removeToolButton)
exportAction <- gtkAction(name='export', label='Export', tooltip='Export results', stock.id='gtk-save')
exportToolButton <- exportAction$createToolItem()
toolbar$add(exportToolButton)
toolbar$add(gtkSeparatorToolItem())
sampleInfoAction <- gtkAction(name='sample.info', label='Samples', tooltip='View sample information', stock.id='gtk-info')
sampleInfoToolButton <- sampleInfoAction$createToolItem()
toolbar$add(sampleInfoToolButton)
mainGroup <- gtkHBox(FALSE, 5)
mainGroup$setBorderWidth(5)
topGroup$packStart(mainGroup)
controlGroup <- gtkVBox(FALSE, 5)
mainGroup$packStart(controlGroup, expand=FALSE, fill=FALSE)
importFrame <- gtkFrame('Data files to use')
controlGroup$packStart(importFrame)
importBox <- gtkVBox(FALSE, 5)
importBox$setBorderWidth(5)
importFrame$add(importBox)
datafileSelect <- gtkHBox(FALSE, 5)
importBox$packStart(datafileSelect)
filesScroll <- gtkScrolledWindow()
datafileSelect$packStart(filesScroll)
files <- gtkTreeView(filelist)
files$insertColumnWithAttributes(position=-1, title='MS datafiles', cell=gtkCellRendererText(), text=0)
files$setHeadersVisible(FALSE)
files['height-request'] <- 100
fileSelect <- files$getSelection()
fileSelect$setMode('multiple')
filesScroll$add(files)
datafileSelectButtons <- gtkVBox(FALSE, 5)
datafileSelect$packStart(datafileSelectButtons, expand=FALSE, fill=FALSE)
fileAddButton <- gtkButton(label='Add')
fileAddButton['width-request'] <- 65
gSignalConnect(fileAddButton, 'clicked', f=function(widget, ...){
file <- gtkFileChooserDialog(title='Select MS datafiles', parent=mainWindow, action='open', 'gtk-ok', GtkResponseType['ok'], 'gtk-cancel', GtkResponseType['cancel'], show=FALSE)
file['select-multiple'] <- TRUE
gSignalConnect(file, 'response', f=function(dialog, response, data){
if(response == GtkResponseType['ok']){
files <- as.character(dialog$getFilenames())
filelist$appendRows(data.frame(Datafiles=files, stringsAsFactors=FALSE))
setwd(dirname(files[1]))
}
dialog$destroy()
})
file$show()
})
fileRemoveButton <- gtkButton(label='Remove')
fileRemoveButton['width-request'] <- 65
fileRemoveButton['sensitive'] <- FALSE
gSignalConnect(fileRemoveButton, 'clicked', f=function(widget, ...){
selected <- sapply(fileSelect$getSelectedRows()$retval, function(x) as.numeric(x$toString())+1)
filelist$setFrame(filelist[-selected, , drop=FALSE])
})
datafileSelectButtons$packStart(fileAddButton, expand=FALSE, fill=FALSE)
datafileSelectButtons$packStart(fileRemoveButton, expand=FALSE, fill=FALSE)
databaseSelect <- gtkHBox(FALSE, 5)
importBox$packStart(databaseSelect, expand=FALSE, fill=FALSE)
database <- gtkEntry()
database['height-request'] <- 24
database$setText('Database fasta file...')
gSignalConnect(database, 'changed', f=function(widget, ...){
validButtons()
})
databaseImport <- gtkButton(label='Browse')
databaseImport['width-request'] <- 65
gSignalConnect(databaseImport, 'clicked', f=function(widget, ...){
file <- gtkFileChooserDialog(title='Select MS datafiles', parent=mainWindow, action='open', 'gtk-ok', GtkResponseType['ok'], 'gtk-cancel', GtkResponseType['cancel'], show=FALSE)
gSignalConnect(file, 'response', f=function(dialog, response, data){
if(response == GtkResponseType['ok']){
file <- as.character(dialog$getFilenames())
database$setText(file)
}
dialog$destroy()
})
file$show()
})
databaseSelect$packStart(database)
databaseSelect$packStart(databaseImport, expand=FALSE, fill=FALSE)
settingsFrame <- gtkFrame('Settings')
controlGroup$packStart(settingsFrame, expand=FALSE, fill=FALSE)
settingsBox <- gtkVBox(FALSE, 15)
settingsBox$setBorderWidth(5)
settingsFrame$add(settingsBox)
settingsSet <- gtkHBox(FALSE, 5)
settingsBox$packStart(settingsSet, expand=FALSE, fill=FALSE)
settingsSetChooser <- gtkComboBoxNewText()
sapply(settingsSetNames, settingsSetChooser$appendText)
settingsSetSaveButton <- gtkButton(label='Save')
settingsSetSaveButton['width-request'] <- 65
settingsSet$packStart(settingsSetChooser)
settingsSet$packStart(settingsSetSaveButton, expand=FALSE, fill=FALSE)
settingsTable <- gtkTable(rows=11, columns=2, homogeneous=FALSE)
settingsTable$setColSpacings(10)
settingsTable$setRowSpacings(10)
settingsBox$packStart(settingsTable)
toleranceLabel <- gtkLabel('Tolerance:')
toleranceLabel['xalign'] <- 1
settingsTable$attach(toleranceLabel, left.attach=0,1, top.attach=0,1)
toleranceBox <- gtkHBox(FALSE, 5)
toleranceValue <- gtkEntry()
toleranceValue['height-request'] <- 24
toleranceValue['width-chars'] <- 5
toleranceValue$setAlignment(1)
toleranceValue$setText(20)
toleranceUnit <- gtkComboBoxNewText()
sapply(c('ppm', 'Da'), toleranceUnit$appendText)
toleranceUnit$setActive(0)
toleranceBox$packStart(toleranceValue, expand=FALSE, fill=FALSE)
toleranceBox$packStart(toleranceUnit, expand=FALSE, fill=FALSE)
settingsTable$attach(toleranceBox, left.attach=1,2, top.attach=0,1)
isotopeErrorLabel <- gtkLabel('Isotope error range:')
isotopeErrorLabel['xalign'] <- 1
settingsTable$attach(isotopeErrorLabel, left.attach=0,1, top.attach=1,2)
isotopeErrorBox <- gtkHBox(FALSE, 5)
isotopeErrorLow <- gtkSpinButton(min=-5, max=10, step=1)
isotopeErrorLow['height-request'] <- 24
isotopeErrorLow['width-chars'] <- 3
isotopeErrorLow$setAlignment(1)
isotopeErrorLow$setValue(0)
gSignalConnect(isotopeErrorLow, 'value-changed', f=function(widget, ...){
min <- widget$getValue()
if(min > isotopeErrorHigh$getValue()){
isotopeErrorHigh$setRange(min, 10)
}
})
isotopeErrorHigh <- gtkSpinButton(min=0, max=10, step=1)
isotopeErrorHigh['height-request'] <- 24
isotopeErrorHigh['width-chars'] <- 3
isotopeErrorHigh$setAlignment(1)
isotopeErrorHigh$setValue(1)
isotopeErrorBox$packStart(isotopeErrorLow, expand=FALSE, fill=FALSE)
isotopeErrorBox$packStart(gtkLabel(' - '), expand=FALSE, fill=FALSE)
isotopeErrorBox$packStart(isotopeErrorHigh, expand=FALSE, fill=FALSE)
settingsTable$attach(isotopeErrorBox, left.attach=1,2, top.attach=1,2)
tdaLabel <- gtkLabel('Target-Decoy:')
tdaLabel['xalign'] <- 1
settingsTable$attach(tdaLabel, left.attach=0,1, top.attach=2,3)
tdaToggle <- gtkCheckButton()
tdaToggle$setActive(TRUE)
settingsTable$attach(tdaToggle, left.attach=1,2, top.attach=2,3)
fragmentationLabel <- gtkLabel('Fragmentation method:')
fragmentationLabel['xalign'] <- 1
settingsTable$attach(fragmentationLabel, left.attach=0,1, top.attach=3,4)
fragmentation <- gtkComboBoxNewText()
sapply(c('From spectrum', 'CID', 'ETD', 'HCD', 'Merge'), fragmentation$appendText)
fragmentation$setActive(0)
settingsTable$attach(fragmentation, left.attach=1,2, top.attach=3,4)
instrumentLabel <- gtkLabel('Instrument:')
instrumentLabel['xalign'] <- 1
settingsTable$attach(instrumentLabel, left.attach=0,1, top.attach=4,5)
instrument <- gtkComboBoxNewText()
sapply(c('Low-res LCQ/LTQ', 'High-res LTQ', 'TOF'), instrument$appendText)
instrument$setActive(0)
settingsTable$attach(instrument, left.attach=1,2, top.attach=4,5)
enzymeLabel <- gtkLabel('Enzyme:')
enzymeLabel['xalign'] <- 1
settingsTable$attach(enzymeLabel, left.attach=0,1, top.attach=5,6)
enzyme <- gtkComboBoxNewText()
sapply(c('Unspecific', 'Trypsin', 'Chymotrypsin', 'Lys-C', 'Lys-N', 'Glu-C', 'Arg-C', 'Asp-N', 'alphaLP', 'None'), enzyme$appendText)
enzyme$setActive(1)
settingsTable$attach(enzyme, left.attach=1,2, top.attach=5,6)
terminiLabel <- gtkLabel('Tolerable termini:')
terminiLabel['xalign'] <- 1
settingsTable$attach(terminiLabel, left.attach=0,1, top.attach=6,7)
terminiBox <- gtkHBox(FALSE, 5)
termini <- gtkSpinButton(min=0, max=2, step=1)
termini$setValue(2)
termini['height-request'] <- 24
termini['width-chars'] <- 3
termini$setAlignment(1)
terminiBox$packStart(termini, expand=FALSE, fill=FALSE)
settingsTable$attach(terminiBox, left.attach=1,2, top.attach=6,7)
modificationLabel <- gtkLabel('Custom modification file:')
modificationLabel['xalign'] <- 1
settingsTable$attach(modificationLabel, left.attach=0,1, top.attach=7,8)
modificationBox <- gtkHBox(FALSE, 5)
modification <- gtkEntry()
modification['height-request'] <- 24
modification['width-chars'] <- 15
modification$setText('Modification file...')
gSignalConnect(modification, 'changed', f=function(widget, ...){
validButtons()
})
modificationImport <- gtkButton(label='Browse')
modificationImport['width-request'] <- 65
gSignalConnect(modificationImport, 'clicked', f=function(widget, ...){
file <- gtkFileChooserDialog(title='Select MS datafiles', parent=mainWindow, action='open', 'gtk-ok', GtkResponseType['ok'], 'gtk-cancel', GtkResponseType['cancel'], show=FALSE)
gSignalConnect(file, 'response', f=function(dialog, response, data){
if(response == GtkResponseType['ok']){
file <- as.character(dialog$getFilenames())
modification$setText(file)
}
dialog$destroy()
})
file$show()
})
modificationBox$packStart(modification)
modificationBox$packStart(modificationImport, expand=FALSE, fill=FALSE)
settingsTable$attach(modificationBox, left.attach=1,2, top.attach=7,8)
lengthLabel <- gtkLabel('Peptide length:')
lengthLabel['xalign'] <- 1
settingsTable$attach(lengthLabel, left.attach=0,1, top.attach=8,9)
lengthBox <- gtkHBox(FALSE, 5)
lengthLow <- gtkSpinButton(min=1, max=100, step=1)
lengthLow['height-request'] <- 24
lengthLow['width-chars'] <- 3
lengthLow$setAlignment(1)
lengthLow$setValue(6)
gSignalConnect(lengthLow, 'value-changed', f=function(widget, ...){
min <- widget$getValue()
if(min > lengthHigh$getValue()){
lengthHigh$setRange(min, 100)
}
})
lengthHigh <- gtkSpinButton(min=6, max=100, step=1)
lengthHigh['height-request'] <- 24
lengthHigh['width-chars'] <- 3
lengthHigh$setAlignment(1)
lengthHigh$setValue(40)
lengthBox$packStart(lengthLow, expand=FALSE, fill=FALSE)
lengthBox$packStart(gtkLabel(' - '), expand=FALSE, fill=FALSE)
lengthBox$packStart(lengthHigh, expand=FALSE, fill=FALSE)
settingsTable$attach(lengthBox, left.attach=1,2, top.attach=8,9)
chargeLabel <- gtkLabel('Peptide charge:')
chargeLabel['xalign'] <- 1
settingsTable$attach(chargeLabel, left.attach=0,1, top.attach=9,10)
chargeBox <- gtkHBox(FALSE, 5)
chargeLow <- gtkSpinButton(min=1, max=10, step=1)
chargeLow['height-request'] <- 24
chargeLow['width-chars'] <- 3
chargeLow$setAlignment(1)
chargeLow$setValue(2)
gSignalConnect(chargeLow, 'value-changed', f=function(widget, ...){
min <- widget$getValue()
if(min > chargeHigh$getValue()){
chargeHigh$setRange(min, 10)
}
})
chargeHigh <- gtkSpinButton(min=2, max=10, step=1)
chargeHigh['height-request'] <- 24
chargeHigh['width-chars'] <- 3
chargeHigh$setAlignment(1)
chargeHigh$setValue(3)
chargeBox$packStart(chargeLow, expand=FALSE, fill=FALSE)
chargeBox$packStart(gtkLabel(' - '), expand=FALSE, fill=FALSE)
chargeBox$packStart(chargeHigh, expand=FALSE, fill=FALSE)
settingsTable$attach(chargeBox, left.attach=1,2, top.attach=9,10)
matchLabel <- gtkLabel('Matches per spectrum:')
matchLabel['xalign'] <- 1
settingsTable$attach(matchLabel, left.attach=0,1, top.attach=10,11)
matchBox <- gtkHBox(FALSE, 5)
match <- gtkSpinButton(min=1, max=100, step=1)
match['height-request'] <- 24
match['width-chars'] <- 3
match$setAlignment(1)
matchBox$packStart(match, expand=FALSE, fill=FALSE)
settingsTable$attach(matchBox, left.attach=1,2, top.attach=10,11)
analyzeBox <- gtkHBox(FALSE, 5)
controlGroup$packStart(analyzeBox, expand=FALSE, fill=FALSE)
analyzeProgress <- gtkProgressBar()
analyzeProgress['height-request'] <- 24
analyzeBox$packStart(analyzeProgress)
analyzeButton <- gtkButton(label='Analyze')
analyzeButton['width-request'] <- 65
analyzeButton['sensitive'] <- FALSE
gSignalConnect(analyzeButton, 'clicked', f=function(widget, ...){
analyzeProgress$setFraction(0)
analyzeButton['sensitive'] <- FALSE
while(gtkEventsPending()){
gtkMainIteration()
}
datafiles <- filelist[]
settings <- collectSettings()
settings$database <- database$getText()
settings$saveMZid <- TRUE
settings$showDecoy <- TRUE
for(i in 1:length(datafiles)){
settings$file <- datafiles[i]
analyzeProgress$setText(basename(settings$file))
while(gtkEventsPending()){
gtkMainIteration()
}
results <- do.call('MSGFplus', settings)
peptide <- strsplit(as.character(results$Peptide), '\\.')
peptide <- unlist(peptide)[seq(2, length(peptide)*3, by=3)]
peptide <- gsub('\\+([\\d]|,)+', '', peptide, perl=TRUE)
results$realPeptide <- peptide
results$'.vis' <- rawFilter(results, sample=sampleFilter(), FDR=FDR$getValue())
rawResults$appendRows(results)
rawUpdated()
mzidFile <- paste(sapply(strsplit(datafiles[i],"\\."), function(x) paste(x[1:(length(x)-1)], collapse=".")), '.mzid', sep='')
sampleInfo <- getRunInfoFromMZID(mzidFile)
updateSampleList(add=sampleInfo)
analyzeProgress$setFraction(i/length(datafiles))
while(gtkEventsPending()){
gtkMainIteration()
}
}
analyzeProgress$setText('Done...')
analyzeButton['sensitive'] <- TRUE
})
analyzeBox$packStart(gtkHBox(), expand=TRUE, fill=TRUE)
analyzeBox$packStart(analyzeButton, expand=FALSE, fill=FALSE)
resultBox <- gtkVBox(FALSE, 5)
resultBox$setSensitive(FALSE)
mainGroup$packStart(resultBox)
filterFrame <- gtkFrame(label='Filters')
filterBox <- gtkHBox(FALSE, 5)
filterBox['border-width'] <- 5
filterFrame$add(filterBox)
resultBox$packStart(filterFrame, expand=FALSE, fill=TRUE)
filterBox$packStart(gtkLabel('Sample:'), expand=FALSE, fill=FALSE)
sampleSelect <- gtkComboBoxNewWithModel(samples)
sampleRenderer <- gtkCellRendererText()
sampleSelect$packStart(sampleRenderer)
sampleSelect$addAttribute(sampleRenderer, 'text', 0)
sampleSelect$setActive(0)
gSignalConnect(sampleSelect, 'changed', f=function(widget, ...){
filterUpdated(FDRChange=FALSE)
})
filterBox$packStart(sampleSelect)
filterBox$packStart(gtkHBox(), expand=TRUE, fill=TRUE)
filterBox$packStart(gtkLabel('FDR cutoff:'), expand=FALSE, fill=FALSE)
FDR <- gtkSpinButton(min=0, max=1, step=0.01)
FDR['width-chars'] <- 5
FDR['height-request'] <- 24
FDR$setValue(0.01)
gSignalConnect(FDR, 'value-changed', f=function(widget, ...){
filterUpdated(SampleChange=FALSE)
})
filterBox$packStart(FDR, expand=FALSE, fill=FALSE)
resultNotebook <- gtkNotebook()
resultNotebook['width-request'] <- 700
resultBox$packStart(resultNotebook)
summaryTab <- gtkHBox(FALSE, 5)
summaryTab['border-width'] <- 5
summaryLeft <- gtkVBox(FALSE, 5)
summaryTab$packStart(summaryLeft)
resultNotebook$appendPage(summaryTab, gtkLabel('Result summary'))
FDRplot <- gtkDrawingArea()
summaryLeft$packStart(FDRplot)
#pepNumberPlot <- gtkDrawingArea()
#summaryLeft$packStart(pepNumberPlot)
#summaryRight <- gtkVBox(FALSE, 5)
#summaryRight['width-request'] <- 100
#summaryTab$packStart(summaryRight)
summaryFrame <- gtkFrame(label='Summary')
summaryLeft$packStart(summaryFrame, expand=FALSE, fill=FALSE)
summaryTable <- gtkTable(rows=2, columns=2, homogeneous=FALSE)
summaryTable['border-width'] <- 5
summaryTable$setColSpacings(10)
summaryTable$setRowSpacings(10)
summaryFrame$add(summaryTable)
nPepIDLabel <- gtkLabel('Identified peptides:')
nPepIDLabel['xalign'] <- 1
summaryTable$attach(nPepIDLabel, left.attach=0,1, top.attach=0,1)
nPepID <- gtkLabel('')
nPepID['xalign'] <- 0
summaryTable$attach(nPepID, left.attach=1,2, top.attach=0,1)
nProtIDLabel <- gtkLabel('Identified proteins:')
nProtIDLabel['xalign'] <- 1
summaryTable$attach(nProtIDLabel, left.attach=0,1, top.attach=1,2)
nProtID <- gtkLabel('')
nProtID['xalign'] <- 0
summaryTable$attach(nProtID, left.attach=1,2, top.attach=1,2)
protIntersectLabel <- gtkLabel('Protein intersection:')
protIntersectLabel['xalign'] <- 1
summaryTable$attach(protIntersectLabel, left.attach=0,1, top.attach=2,3)
protIntersect <- gtkLabel('')
protIntersect['xalign'] <- 0
summaryTable$attach(protIntersect, left.attach=1,2, top.attach=2,3)
chargeLabel <- gtkLabel('Charge:')
chargeLabel['xalign'] <- 1
chargeLabel['yalign'] <- 0
summaryTable$attach(chargeLabel, left.attach=0,1, top.attach=3,4)
charge <- gtkLabel('\t(min)\n\t(median)\n\t(max)')
charge['xalign'] <- 0
summaryTable$attach(charge, left.attach=1,2, top.attach=3,4)
peptideTab <- gtkHBox(FALSE, 5)
peptideTab['border-width'] <- 5
peptideScroll <- gtkScrolledWindow()
peptideTab$packStart(peptideScroll)
peptide <- gtkTreeView(peptides)
peptide$insertColumnWithAttributes(position=-1, title='Peptides', cell=gtkCellRendererText(), text=0)
peptideSelection <- peptide$getSelection()
gSignalConnect(peptide, 'cursor-changed', function(...){
peptideSelected <- with(peptideSelection$getSelected(), model$getValue(iter, 0)$value)
pepInfo <- createPeptideView(peptideSelected)
if(!is.null(peptideViewScroll$getChild())) peptideViewScroll$getChild()$destroy()
peptideViewScroll$add(createPeptideView(peptideSelected))
})
peptideScroll$add(peptide)
peptideViewFrame <- gtkFrame('Information')
peptideTab$packStart(peptideViewFrame)
peptideViewScroll <- gtkScrolledWindow()
peptideViewScroll['border-width'] <- 5
peptideViewScroll$setPolicy(hscrollbar.policy=GtkPolicyType[2], vscrollbar.policy=GtkPolicyType[1])
peptideViewFrame$add(peptideViewScroll)
resultNotebook$appendPage(peptideTab, gtkLabel('Peptides'))
proteinTab <- gtkVBox(FALSE, 5)
proteinTab['border-width'] <- 5
proteinTopBox <- gtkHBox(FALSE, 5)
proteinTab$packStart(proteinTopBox)
proteinScroll <- gtkScrolledWindow()
proteinTopBox$packStart(proteinScroll)
protein <- gtkTreeView(proteins)
protein$insertColumnWithAttributes(position=-1, title='Protein', cell=gtkCellRendererText(), text=0)
proteinScroll$add(protein)
proteinSelect <- protein$getSelection()
gSignalConnect(protein, 'cursor-changed', f=function(...){
proteinName <- with(proteinSelect$getSelected(), model$getValue(iter, 0)$value)
proteinSequenceFromDB <- findProteinSequence(proteinName)
if(sampleFilter() == 'All'){
evidenceList <- findProteinEvidence(proteinName, FDR=FDR$getValue())
} else {
evidenceList <- findProteinEvidence(proteinName, sample=sampleFilter(), FDR=FDR$getValue())
}
evidenceLocation <- findProteinEvidenceLocation(proteinSequenceFromDB[[1]]$sequence, evidenceList, collate=FALSE)
tempPeptideSelection$unselectAll()
nPeptideValue$setText(length(evidenceList))
coverageValue$setText(paste(sprintf('%.1f', 100*length(unique(unlist(lapply(evidenceLocation, function(x) x[1]:x[2]))))/nchar(proteinSequenceFromDB[[1]]$sequence)), '%'))
protLengthValue$setText(nchar(proteinSequenceFromDB[[1]]$sequence))
protMassValue$setText(paste(sprintf('%.2f', pepMass(proteinSequenceFromDB[[1]]$sequence)), 'Da'))
protPIValue$setText(sprintf('%.2f', peppI(proteinSequenceFromDB[[1]]$sequence)))
hydroValue$setText(sprintf('%.1f', Qval(proteinSequenceFromDB[[1]]$sequence)))
tempPeptideList$setFrame(data.frame(Peptides=paste(sapply(evidenceLocation, '[', 1), '-', sapply(evidenceLocation, '[', 2), ': ', names(evidenceList), sep=''), stringsAsFactors=FALSE))
tempSampleList$setFrame(data.frame(Samples=unique(rawResults[rawResults[, 'Protein'] == proteinName, 'SpecFile']), stringsAsFactors=FALSE))
sequenceLabel$setMarkup(formatProteinPango(proteinSequenceFromDB[[1]]$sequence, evidenceList))
})
proteinTopBoxRight <- gtkVBox(FALSE, 5)
proteinTopBox$packStart(proteinTopBoxRight)
proteinPeptideScroll <- gtkScrolledWindow()
proteinTopBoxRight$packStart(proteinPeptideScroll)
tempPeptide <- gtkTreeView(tempPeptideList)
tempPeptide$insertColumnWithAttributes(position=-1, title='Peptide', cell=gtkCellRendererText(), text=0)
gSignalConnect(tempPeptide, 'cursor-changed', f=function(...){
proteinName <- with(proteinSelect$getSelected(), model$getValue(iter, 0)$value)
proteinSequenceFromDB <- findProteinSequence(proteinName)
if(sampleFilter() == 'All'){
evidenceList <- findProteinEvidence(proteinName, FDR=FDR$getValue())
} else {
evidenceList <- findProteinEvidence(proteinName, sample=sampleFilter(), FDR=FDR$getValue())
}
evidenceSelection <- as.numeric(with(tempPeptideSelection$getSelected(), model$getPath(iter))$toString())+1
sequenceLabel$setMarkup(formatProteinPango(proteinSequenceFromDB[[1]]$sequence, evidenceList, evidenceSelection))
})
gSignalConnect(tempPeptide, 'row-activated', function(...){
selectedSequence <- strsplit(with(tempPeptideSelection$getSelected(), model$getValue(iter, 0)$value), ' ')[[1]][2]
peptidePath <- gtkTreePathNewFromString(which(peptides[] == selectedSequence)-1)
resultNotebook$setCurrentPage(resultNotebook$pageNum(peptideTab))
peptideSelection$selectPath(peptidePath)
peptide$scrollToCell(peptidePath, use.align=TRUE, row.align=0.5)
gSignalEmit(peptide, 'cursor-changed')
})
tempPeptideSelection <- tempPeptide$getSelection()
proteinPeptideScroll$add(tempPeptide)
proteinSampleScroll <- gtkScrolledWindow()
proteinTopBoxRight$packStart(proteinSampleScroll)
tempSamples <- gtkTreeView(tempSampleList)
tempSamples$insertColumnWithAttributes(position=-1, title='Samples', cell=gtkCellRendererText(), text=0)
proteinSampleScroll$add(tempSamples)
proteinBottomBox <- gtkHBox(FALSE, 5)
proteinTab$packStart(proteinBottomBox, expand=FALSE, fill=FALSE)
proteinSequence <- gtkFrame('Sequence:')
proteinSequenceScroll <- gtkScrolledWindow()
proteinSequenceScroll['border-width'] <- 5
proteinSequenceScroll['vscrollbar-policy'] <- GtkPolicyType[1]
proteinSequenceScroll['hscrollbar-policy'] <- GtkPolicyType[3]
proteinSequence$add(proteinSequenceScroll)
sequenceLabel <- gtkLabel()
sequenceLabel['selectable'] <- TRUE
sequenceLabel$setLineWrap(TRUE)
sequenceLabel$setLineWrapMode('PANGO_WRAP_WORD')
font_descr <- pangoFontDescriptionNew()
font_descr$setFamily('courier')
sequenceLabel$modifyFont(font_descr)
proteinSequenceScroll$addWithViewport(sequenceLabel)
proteinSequenceScroll$getChild()$setShadowType(GtkShadowType[1])
proteinBottomBox$packStart(proteinSequence, expand=FALSE, fill=FALSE)
proteinInformationFrame <- gtkFrame('Information:')
proteinInformationTable <- gtkTable(rows=8, columns=2, homogeneous=FALSE)
proteinInformationTable['border-width'] <- 5
nPeptideLabel <- gtkLabel('Number of detected peptides:')
nPeptideLabel['xalign'] <- 1
proteinInformationTable$attach(nPeptideLabel, left.attach=0,1, top.attach=0,1)
nPeptideValue <- gtkLabel()
nPeptideValue['xalign'] <- 0
proteinInformationTable$attach(nPeptideValue, left.attach=1,2, top.attach=0,1)
coverageLabel <- gtkLabel('Coverage:')
coverageLabel['xalign'] <- 1
proteinInformationTable$attach(coverageLabel, left.attach=0,1, top.attach=1,2)
coverageValue <- gtkLabel()
coverageValue['xalign'] <- 0
proteinInformationTable$attach(coverageValue, left.attach=1,2, top.attach=1,2)
protLengthLabel <- gtkLabel('Length (residues):')
protLengthLabel['xalign'] <- 1
proteinInformationTable$attach(protLengthLabel, left.attach=0,1, top.attach=2,3)
protLengthValue <- gtkLabel()
protLengthValue['xalign'] <- 0
proteinInformationTable$attach(protLengthValue, left.attach=1,2, top.attach=2,3)
protMassLabel <- gtkLabel('Mass:')
protMassLabel['xalign'] <- 1
proteinInformationTable$attach(protMassLabel, left.attach=0,1, top.attach=3,4)
protMassValue <- gtkLabel()
protMassValue['xalign'] <- 0
proteinInformationTable$attach(protMassValue, left.attach=1,2, top.attach=3,4)
protPILabel <- gtkLabel('Isoelectric point (pI):')
protPILabel['xalign'] <- 1
proteinInformationTable$attach(protPILabel, left.attach=0,1, top.attach=4,5)
protPIValue <- gtkLabel()
protPIValue['xalign'] <- 0
proteinInformationTable$attach(protPIValue, left.attach=1,2, top.attach=4,5)
hydroLabel <- gtkLabel('Hydrophobicity (Q Value):')
hydroLabel['xalign'] <- 1
proteinInformationTable$attach(hydroLabel, left.attach=0,1, top.attach=5,6)
hydroValue <- gtkLabel()
hydroValue['xalign'] <- 0
proteinInformationTable$attach(hydroValue, left.attach=1,2, top.attach=5,6)
blastButton <- gtkButton('BLAST')
blastButton['width-request'] <- 80
blastButton['height-request'] <- 40
gSignalConnect(blastButton, 'clicked', f=function(...){
sequence <- findProteinSequence(with(proteinSelect$getSelected(), model$getValue(iter, 0)$value))
RID <- blastPut(sequence[[1]]$sequence, db='nr')
while(blastCheck(RID) != 'READY'){
Sys.sleep(5)
if(blastCheck(RID) != 'WAITING'){
stop('Unknown problem occured')
}
}
blastGet(RID)
})
proteinInformationTable$attach(blastButton, left.attach=0,2, top.attach=6,8, xoptions='', yoptions='')
proteinInformationTable$setRowSpacings(15)
proteinInformationTable$setColSpacings(5)
proteinInformationFrame$add(proteinInformationTable)
proteinBottomBox$packStart(proteinInformationFrame)
resultNotebook$appendPage(proteinTab, gtkLabel('Proteins'))
rawTab <- gtkVBox(FALSE, 5)
rawTab['border-width'] <- 5
rawExpander <- gtkExpander(label='Spectrum plot')
rawPlotAndSettingsBox <- gtkVBox(FALSE, 5)
rawExpander$add(rawPlotAndSettingsBox)
rawSettingsExpander <- gtkExpander(label='Settings')
rawSettingsExpander['border-width'] <- 5
rawSettingsBox <- gtkHBox(FALSE, 5)
rawSettingsBox$packStart(gtkHBox(), expand=TRUE, fill=TRUE)
rawSettingsTable <- gtkTable(rows=3, columns=7, homogeneous=FALSE)
rawSettingsTable$setColSpacing(0, 5)
rawSettingsTable$setColSpacing(1, 70)
rawSettingsTable$setColSpacing(2, 5)
ppmLabel <- gtkLabel('ppm: ')
ppmLabel['xalign'] <- 1
rawSettingsTable$attach(ppmLabel, left.attach=0,1, top.attach=0,1)
ppmPlotSetting <- gtkEntry()
ppmPlotSetting$setText('20')
ppmPlotSetting['height-request'] <- 24
ppmPlotSetting['width-request'] <- 40
gSignalConnect(ppmPlotSetting, 'activate', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(ppmPlotSetting, left.attach=1,2, top.attach=0,1)
neutralLabel <- gtkLabel('Neutral losses: ')
neutralLabel['xalign'] <- 1
rawSettingsTable$attach(neutralLabel, left.attach=0,1, top.attach=1,2)
neutralPlotSetting <- gtkCheckButton()
neutralPlotSetting$setActive(TRUE)
gSignalConnect(neutralPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(neutralPlotSetting, left.attach=1,2, top.attach=1,2)
traceLabel <- gtkLabel('Ion trace: ')
traceLabel['xalign'] <- 1
rawSettingsTable$attach(traceLabel, left.attach=0,1, top.attach=2,3)
tracePlotSetting <- gtkCheckButton()
tracePlotSetting$setActive(TRUE)
gSignalConnect(tracePlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(tracePlotSetting, left.attach=1,2, top.attach=2,3)
ionsLabel <- gtkLabel('Ions:')
ionsLabel['xalign'] <- 1
rawSettingsTable$attach(ionsLabel, left.attach=2,3, top.attach=0,1)
aIonLabel <- gtkLabel('a:')
aIonLabel['xalign'] <- 1
rawSettingsTable$attach(aIonLabel, left.attach=3,4, top.attach=0,1)
aIonPlotSetting <- gtkCheckButton()
aIonPlotSetting$setActive(TRUE)
gSignalConnect(aIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(aIonPlotSetting, left.attach=4,5, top.attach=0,1)
bIonLabel <- gtkLabel('b:')
bIonLabel['xalign'] <- 1
rawSettingsTable$attach(bIonLabel, left.attach=3,4, top.attach=1,2)
bIonPlotSetting <- gtkCheckButton()
bIonPlotSetting$setActive(TRUE)
gSignalConnect(bIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(bIonPlotSetting, left.attach=4,5, top.attach=1,2)
cIonLabel <- gtkLabel('c:')
cIonLabel['xalign'] <- 1
rawSettingsTable$attach(cIonLabel, left.attach=3,4, top.attach=2,3)
cIonPlotSetting <- gtkCheckButton()
gSignalConnect(cIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(cIonPlotSetting, left.attach=4,5, top.attach=2,3)
xIonLabel <- gtkLabel('x:')
xIonLabel['xalign'] <- 1
rawSettingsTable$attach(xIonLabel, left.attach=5,6, top.attach=0,1)
xIonPlotSetting <- gtkCheckButton()
gSignalConnect(xIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(xIonPlotSetting, left.attach=6,7, top.attach=0,1)
yIonLabel <- gtkLabel('y:')
yIonLabel['xalign'] <- 1
rawSettingsTable$attach(yIonLabel, left.attach=5,6, top.attach=1,2)
yIonPlotSetting <- gtkCheckButton()
yIonPlotSetting$setActive(TRUE)
gSignalConnect(yIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(yIonPlotSetting, left.attach=6,7, top.attach=1,2)
zIonLabel <- gtkLabel('z:')
zIonLabel['xalign'] <- 1
rawSettingsTable$attach(zIonLabel, left.attach=5,6, top.attach=2,3)
zIonPlotSetting <- gtkCheckButton()
gSignalConnect(zIonPlotSetting, 'toggled', f=function(...){
selection <- rawSelect$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!samples[samples[,'Samples']==sample, 'loaded']){
raw$setData(key='msConnection', data=openMSfile(samples[samples[,'Samples']==sample, 'msfile']))
samples[samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
rawExpander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=raw$getData('msConnection'), scan=scan, seq=seq, device=spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
})
rawSettingsTable$attach(zIonPlotSetting, left.attach=6,7, top.attach=2,3)
rawSettingsBox$packStart(rawSettingsTable)
rawSettingsBox$packStart(gtkHBox(), expand=TRUE, fill=TRUE)
rawSettingsExpander$add(rawSettingsBox)
rawPlotAndSettingsBox$packStart(rawSettingsExpander)
rawTab$packStart(rawExpander, expand=FALSE, fill=FALSE)
rawPlotBox <- gtkVBox(FALSE, 5)
rawPlotBox['height-request'] <- 400
rawPlotAndSettingsBox$packStart(rawPlotBox)
rawExpander$setExpanded(TRUE)
spectrumPlot <- gtkDrawingArea()
rawPlotBox$packStart(spectrumPlot)
rawScroll <- gtkScrolledWindow()
rawTab$packStart(rawScroll)
raw <- gtkTreeView(rawResultsFilter)
for(i in 1:(ncol(rawResults)-2)){
raw$insertColumnWithAttributes(position=-1, title=dimnames(rawResults)[[2]][i], cell=gtkCellRendererText(), text=i-1)
}
rawSelect <- raw$getSelection()
rawScroll$add(raw)
gSignalConnect(raw, 'row-activated', f=function(treeview, path, column, user.data){
model <- treeview$getModel()
selection <- model$getIter(path)$iter
sample <- treeview$getModel()$getValue(selection, 0)$value
if(!user.data$samples[user.data$samples[,'Samples']==sample, 'loaded']){
treeview$setData(key='msConnection', data=openMSfile(user.data$samples[user.data$samples[,'Samples']==sample, 'rawfile']))
user.data$samples[user.data$samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- model$getValue(selection, 2)$value
seq <- model$getValue(selection, 16)$value
user.data$expander$setExpanded(TRUE)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=treeview$getData('msConnection'), scan=scan, seq=seq, device=user.data$spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
treeview$scrollToCell(path)
}, data=list(samples=samples, expander=rawExpander, spectrumPlot=spectrumPlot))
gSignalConnect(rawSelect, 'changed', f=function(select, user.data){
if(rawExpander$getExpanded()){
selection <- select$getSelected()
sample <- with(selection, model$getValue(iter, 0)$value)
if(!user.data$samples[user.data$samples[,'Samples']==sample, 'loaded']){
user.data$raw$setData(key='msConnection', data=openMSfile(user.data$samples[user.data$samples[,'Samples']==sample, 'rawfile']))
user.data$samples[user.data$samples[,'Samples']==sample, 'loaded'] <- TRUE
} else {}
scan <- with(selection, model$getValue(iter, 2)$value)
seq <- with(selection, model$getValue(iter, 16)$value)
plotSettings <- collectRawPlotSettings()
plotSpectrum(data=user.data$raw$getData('msConnection'), scan=scan, seq=seq, device=user.data$spectrumPlot$getData('Device'), ppm=plotSettings$ppm, ionTrace=plotSettings$ionTrace, ions=plotSettings$ions, neutralLosses=plotSettings$neutralLosses)
} else {}
}, data=list(samples=samples, raw=raw, spectrumPlot=spectrumPlot))
resultNotebook$appendPage(rawTab, gtkLabel('Raw data'))
statusbar <- gtkStatusbar()
topGroup$packStart(statusbar, expand=FALSE, fill=FALSE)
mainWindow$show()
asCairoDevice(FDRplot)
FDRplot$setData(key='Device', data=dev.cur())
grid.newpage()
#asCairoDevice(pepNumberPlot)
#pepNumberPlot$setData(key='Device', data=dev.cur())
resultNotebook$setCurrentPage(3)
asCairoDevice(spectrumPlot)
spectrumPlot$setData(key='Device', data=dev.cur())
grid.newpage()
resultNotebook$setCurrentPage(0)
rawExpander$setExpanded(FALSE)
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