def __initVars(self):
self.firstLoad = True
self.colorIndex = 0
self.txtColor = None
self.curDir = os.getcwd()
self.peakTableName = None
self.curParamDict = None
self.curTypeDict = None
self.fileList = None
# self.Rliblist = ['xcms']
# self.Rlibs = initRlibs(self.Rliblist)
self.xcmsOK = False
self.eicPlot = self.plotWidget.canvas.axDict['ax1']
self.eicList = []
self.eicDict = None
self.eicClass = None
self.curXSET = None
self.plotIndex = 0
self.initIndex = 0
self.ignoreSignal = False
self.highlighter = PH(self.batchScriptTE.document())
self.rThread = XCMSThread(self)
# self.rProcess = QtCore.QProcess()
'''
findPeaks.matchedFilter(object, fwhm = 30, sigma = fwhm/2.3548, max = 5,
snthresh = 10, step = 0.1, steps = 2, mzdiff = 0.8 - step*steps,
index = FALSE, sleep = 0)
object --xcmsRaw object
fwhm --full width at half maximum of matched filtration gaussian model peak
sigma --standard deviation of matched filtration model peak
max --maximum number of peaks per extracted ion chromatogram
snthresh --signal to noise ratio cutoff
step --step size to use for profile generation
steps --number of steps to merge prior to filtration
mzdiff --minimum difference in m/z for peaks with overlapping retention times
index --return indicies instead of values for m/z and retention times
sleep --number of seconds to pause between plotting peak finding cycles
'''
self.matchedFilterParams = {'fwhm':30.,
'sigma':30/2.3548,
'max': 5.,
'snthresh':10.,
'step':0.01,
'steps':2.,
'mzdiff':0.01,
}
self.matchedFilterTypes = {'fwhm':float,
'sigma':float,
'max':float,
'snthresh':float,
'step':float,
'steps':float,
'mzdiff':float
}
##########################
'''
CentWave
object = "xcmsRaw"
findPeaks.centWave(object, ppm=25, peakwidth=c(20,50),
snthresh=10, prefilter=c(3,100), integrate=1, mzdiff=-0.001,
fitgauss=FALSE, scanrange= numeric(), sleep=0, verbose.columns=FALSE)
object --xcmsSet objectprint methodHelp
ppm --maxmial tolerated m/z deviation in consecutive scans, in ppm (parts per million)
peakwidth --Chromatographic peak width, given as range (min,max) in seconds
snthresh --signal to noise ratio cutoff, definition see below.
prefilter --prefilter=c(k,I). Prefilter step for the first phase. Mass traces are only retained if they contain at least k peaks with intensity >= I.
integrate --Integration method. If =1 peak limits are found through descent on the mexican hat filtered data, if =2 the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.
mzdiff --minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap
fitgauss --logical, if TRUE a Gaussian is fitted to each peak
scanrange --scan range to process
sleep --number of seconds to pause between plotting peak finding cycles
verbose.columns logical, if TRUE additional peak meta data columns are returned
'''
#this method is not working well yet for the ORBITRAP DATA ACQUIRED AT PNNL
self.centWaveParams = {'ppm': 10.,
'peakwidth': str([20,50]),#this needs to be fixed, the new version of PyQt4 handles this better
'snthresh':10.,
'prefilter':str([3,100]),
'mzdiff':-0.001,
}
self.centWaveTypes = {'ppm': float,
'peakwidth': str,
'snthresh':float,
'prefilter':str,
'mzdiff':float,
}
################################
self.groupParams = {'bw':30.,
'minfrac':0.1,
'mzwid':0.1,
'max':3
}
self.groupTypes = {'bw':float,
'minfrac':float,
'mzwid':float,
'max':int
}
##############################
self.retcorParams = {'extra':2,
'span':0.5,
'f':'symmetric',
'plottype':'none',
'missing':2
}
self.retcorTypes = {'extra':int,
'span':float,
'f':str,
'plottype':str,
'missing':str
}
#########################
self.xcmsParamDict = {'Matched Filter':self.matchedFilterParams,
'Group Params':self.groupParams,
'Retcor Params':self.retcorParams,
'CentWave':self.centWaveParams}
self.xcmsTypeDict = {'Matched Filter':self.matchedFilterTypes,
'Group Params':self.groupTypes,
'Retcor Params':self.retcorTypes,
'CentWave':self.centWaveTypes}
def __initVars(self):
self.firstLoad = True
self.colorIndex = 0
self.txtColor = None
self.curDir = os.getcwd()
self.peakTableName = None
self.curParamDict = None
self.curTypeDict = None
self.fileList = None
# self.Rliblist = ['xcms']
# self.Rlibs = initRlibs(self.Rliblist)
self.xcmsOK = False
self.eicPlot = self.plotWidget.canvas.axDict['ax1']
self.eicList = []
self.eicDict = None
self.eicClass = None
self.curXSET = None
self.plotIndex = 0
self.initIndex = 0
self.ignoreSignal = False
self.highlighter = PH(self.batchScriptTE.document())
self.rThread = XCMSThread(self)
# self.rProcess = QtCore.QProcess()
'''
findPeaks.matchedFilter(object, fwhm = 30, sigma = fwhm/2.3548, max = 5,
snthresh = 10, step = 0.1, steps = 2, mzdiff = 0.8 - step*steps,
index = FALSE, sleep = 0)
object --xcmsRaw object
fwhm --full width at half maximum of matched filtration gaussian model peak
sigma --standard deviation of matched filtration model peak
max --maximum number of peaks per extracted ion chromatogram
snthresh --signal to noise ratio cutoff
step --step size to use for profile generation
steps --number of steps to merge prior to filtration
mzdiff --minimum difference in m/z for peaks with overlapping retention times
index --return indicies instead of values for m/z and retention times
sleep --number of seconds to pause between plotting peak finding cycles
'''
self.matchedFilterParams = {
'fwhm': 30.,
'sigma': 30 / 2.3548,
'max': 5.,
'snthresh': 10.,
'step': 0.01,
'steps': 2.,
'mzdiff': 0.01,
}
self.matchedFilterTypes = {
'fwhm': float,
'sigma': float,
'max': float,
'snthresh': float,
'step': float,
'steps': float,
'mzdiff': float
}
##########################
'''
CentWave
object = "xcmsRaw"
findPeaks.centWave(object, ppm=25, peakwidth=c(20,50),
snthresh=10, prefilter=c(3,100), integrate=1, mzdiff=-0.001,
fitgauss=FALSE, scanrange= numeric(), sleep=0, verbose.columns=FALSE)
object --xcmsSet objectprint methodHelp
ppm --maxmial tolerated m/z deviation in consecutive scans, in ppm (parts per million)
peakwidth --Chromatographic peak width, given as range (min,max) in seconds
snthresh --signal to noise ratio cutoff, definition see below.
prefilter --prefilter=c(k,I). Prefilter step for the first phase. Mass traces are only retained if they contain at least k peaks with intensity >= I.
integrate --Integration method. If =1 peak limits are found through descent on the mexican hat filtered data, if =2 the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.
mzdiff --minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap
fitgauss --logical, if TRUE a Gaussian is fitted to each peak
scanrange --scan range to process
sleep --number of seconds to pause between plotting peak finding cycles
verbose.columns logical, if TRUE additional peak meta data columns are returned
'''
#this method is not working well yet for the ORBITRAP DATA ACQUIRED AT PNNL
self.centWaveParams = {
'ppm': 10.,
'peakwidth': str(
[20, 50]
), #this needs to be fixed, the new version of PyQt4 handles this better
'snthresh': 10.,
'prefilter': str([3, 100]),
'mzdiff': -0.001,
}
self.centWaveTypes = {
'ppm': float,
'peakwidth': str,
'snthresh': float,
'prefilter': str,
'mzdiff': float,
}
################################
self.groupParams = {'bw': 30., 'minfrac': 0.1, 'mzwid': 0.1, 'max': 3}
self.groupTypes = {
'bw': float,
'minfrac': float,
'mzwid': float,
'max': int
}
##############################
self.retcorParams = {
'extra': 2,
'span': 0.5,
'f': 'symmetric',
'plottype': 'none',
'missing': 2
}
self.retcorTypes = {
'extra': int,
'span': float,
'f': str,
'plottype': str,
'missing': str
}
#########################
self.xcmsParamDict = {
'Matched Filter': self.matchedFilterParams,
'Group Params': self.groupParams,
'Retcor Params': self.retcorParams,
'CentWave': self.centWaveParams
}
self.xcmsTypeDict = {
'Matched Filter': self.matchedFilterTypes,
'Group Params': self.groupTypes,
'Retcor Params': self.retcorTypes,
'CentWave': self.centWaveTypes
}
class pyXCMSWindow(QtGui.QMainWindow, ui_main.Ui_MainWindow):
def __init__(self, parent = None):
super(pyXCMSWindow, self).__init__(parent)
self.ui = self.setupUi(self)
self.__initVars()
self.__initConnections()
self._setContext_()
self.setupGUI()
self.setupR()
def __initVars(self):
self.firstLoad = True
self.colorIndex = 0
self.txtColor = None
self.curDir = os.getcwd()
self.peakTableName = None
self.curParamDict = None
self.curTypeDict = None
self.fileList = None
# self.Rliblist = ['xcms']
# self.Rlibs = initRlibs(self.Rliblist)
self.xcmsOK = False
self.eicPlot = self.plotWidget.canvas.axDict['ax1']
self.eicList = []
self.eicDict = None
self.eicClass = None
self.curXSET = None
self.plotIndex = 0
self.initIndex = 0
self.ignoreSignal = False
self.highlighter = PH(self.batchScriptTE.document())
self.rThread = XCMSThread(self)
# self.rProcess = QtCore.QProcess()
'''
findPeaks.matchedFilter(object, fwhm = 30, sigma = fwhm/2.3548, max = 5,
snthresh = 10, step = 0.1, steps = 2, mzdiff = 0.8 - step*steps,
index = FALSE, sleep = 0)
object --xcmsRaw object
fwhm --full width at half maximum of matched filtration gaussian model peak
sigma --standard deviation of matched filtration model peak
max --maximum number of peaks per extracted ion chromatogram
snthresh --signal to noise ratio cutoff
step --step size to use for profile generation
steps --number of steps to merge prior to filtration
mzdiff --minimum difference in m/z for peaks with overlapping retention times
index --return indicies instead of values for m/z and retention times
sleep --number of seconds to pause between plotting peak finding cycles
'''
self.matchedFilterParams = {'fwhm':30.,
'sigma':30/2.3548,
'max': 5.,
'snthresh':10.,
'step':0.01,
'steps':2.,
'mzdiff':0.01,
}
self.matchedFilterTypes = {'fwhm':float,
'sigma':float,
'max':float,
'snthresh':float,
'step':float,
'steps':float,
'mzdiff':float
}
##########################
'''
CentWave
object = "xcmsRaw"
findPeaks.centWave(object, ppm=25, peakwidth=c(20,50),
snthresh=10, prefilter=c(3,100), integrate=1, mzdiff=-0.001,
fitgauss=FALSE, scanrange= numeric(), sleep=0, verbose.columns=FALSE)
object --xcmsSet objectprint methodHelp
ppm --maxmial tolerated m/z deviation in consecutive scans, in ppm (parts per million)
peakwidth --Chromatographic peak width, given as range (min,max) in seconds
snthresh --signal to noise ratio cutoff, definition see below.
prefilter --prefilter=c(k,I). Prefilter step for the first phase. Mass traces are only retained if they contain at least k peaks with intensity >= I.
integrate --Integration method. If =1 peak limits are found through descent on the mexican hat filtered data, if =2 the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.
mzdiff --minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap
fitgauss --logical, if TRUE a Gaussian is fitted to each peak
scanrange --scan range to process
sleep --number of seconds to pause between plotting peak finding cycles
verbose.columns logical, if TRUE additional peak meta data columns are returned
'''
#this method is not working well yet for the ORBITRAP DATA ACQUIRED AT PNNL
self.centWaveParams = {'ppm': 10.,
'peakwidth': str([20,50]),#this needs to be fixed, the new version of PyQt4 handles this better
'snthresh':10.,
'prefilter':str([3,100]),
'mzdiff':-0.001,
}
self.centWaveTypes = {'ppm': float,
'peakwidth': str,
'snthresh':float,
'prefilter':str,
'mzdiff':float,
}
################################
self.groupParams = {'bw':30.,
'minfrac':0.1,
'mzwid':0.1,
'max':3
}
self.groupTypes = {'bw':float,
'minfrac':float,
'mzwid':float,
'max':int
}
##############################
self.retcorParams = {'extra':2,
'span':0.5,
'f':'symmetric',
'plottype':'none',
'missing':2
}
self.retcorTypes = {'extra':int,
'span':float,
'f':str,
'plottype':str,
'missing':str
}
#########################
self.xcmsParamDict = {'Matched Filter':self.matchedFilterParams,
'Group Params':self.groupParams,
'Retcor Params':self.retcorParams,
'CentWave':self.centWaveParams}
self.xcmsTypeDict = {'Matched Filter':self.matchedFilterTypes,
'Group Params':self.groupTypes,
'Retcor Params':self.retcorTypes,
'CentWave':self.centWaveTypes}
def __initConnections(self):
QtCore.QObject.connect(self.getFolderBtn, QtCore.SIGNAL("clicked()"), self.initFileList)
QtCore.QObject.connect(self.xcmsMethodCB, QtCore.SIGNAL("currentIndexChanged(QString)"), self.updateParamTable)
QtCore.QObject.connect(self.paramTableWidget, QtCore.SIGNAL("itemDoubleClicked(QTableWidgetItem*)"), self.paramTableEntered)
QtCore.QObject.connect(self.paramTableWidget, QtCore.SIGNAL("itemChanged(QTableWidgetItem*)"), self.paramTableChanged)
QtCore.QObject.connect(self.paramTableWidget, QtCore.SIGNAL("helpRequested(PyQt_PyObject)"), self.showParamHelp)
QtCore.QObject.connect(self.actionTest_XCMS, QtCore.SIGNAL("triggered()"), self.testXCMS)
QtCore.QObject.connect(self.actionSave_HDF5, QtCore.SIGNAL("triggered()"), self.saveEICs2HDF5)
QtCore.QObject.connect(self.actionLoad_HDF5, QtCore.SIGNAL("triggered()"), self.loadHDF52EICs)
QtCore.QObject.connect(self.actionSave_Results_Table, QtCore.SIGNAL("triggered()"), self.saveXCMSResultsCSV)
QtCore.QObject.connect(self.getEICBtn, QtCore.SIGNAL("clicked()"), self.fetchEIC)
QtCore.QObject.connect(self.runXCMSBtn, QtCore.SIGNAL("clicked()"), self.startXCMSRun)
QtCore.QObject.connect(self.loadRPY2BatchBtn, QtCore.SIGNAL("clicked()"), self.loadRPY2Batch)
QtCore.QObject.connect(self.eicIndexSB, QtCore.SIGNAL("valueChanged(int)"), self.indexChanged)
QtCore.QObject.connect(self.rThread, QtCore.SIGNAL("xcmsOutUpdate(PyQt_PyObject)"), self.updateROutput)
QtCore.QObject.connect(self.rThread, QtCore.SIGNAL("xcmsGetEIC(PyQt_PyObject)"), self.getThreadEIC)
QtCore.QObject.connect(self.rThread, QtCore.SIGNAL("xcmsSet(PyQt_PyObject)"), self.setXCMSGroup)
self.removeFileAction = QtGui.QAction("Remove File", self)
self.dirListWidget.addAction(self.removeFileAction)
QtCore.QObject.connect(self.removeFileAction,QtCore.SIGNAL("triggered()"), self.removeFile)
self.removeEICAction = QtGui.QAction("Remove EIC", self)
self.plotWidget.addAction(self.removeEICAction)
QtCore.QObject.connect(self.removeEICAction,QtCore.SIGNAL("triggered()"), self.removeEIC)
def removeEIC(self):
print "Remove EIC"
self.curIndex = self.plotIndex#need to do this because the slider is going from 1 and python counts from 0
self.eicClass.eicTraces.pop(self.curIndex)
self.eicClass.numEICs = self.eicClass.numEICs-1
numEICs = self.eicClass.numEICs
self.eicIndexSlider.setMaximum(numEICs-1)
self.eicIndexSB.setMaximum(numEICs-1)
self.eicIndexSB.setValue(self.curIndex-1)#just to be safe
def removeFile(self):
selItem = self.dirListWidget.selectedItems()[0]
curRow = self.dirListWidget.row(selItem)
print curRow
self.dirListWidget.takeItem(curRow)
self.dirList.pop(curRow)
print len(self.dirList)
def _setContext_(self):
self.plotWidget.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.plotWidget.connect(self.plotWidget, QtCore.SIGNAL("customContextMenuRequested(QPoint)"), self._plotContext_)
self.dirListWidget.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.dirListWidget.connect(self.dirListWidget, QtCore.SIGNAL("customContextMenuRequested(QPoint)"), self._dirListContext_)
def _dirListContext_(self, point):
ct_menu = QtGui.QMenu("File List Menu", self.dirListWidget)
ct_menu.addAction(self.removeFileAction)
ct_menu.exec_(self.dirListWidget.mapToGlobal(point))
def _plotContext_(self, point):
ct_menu = QtGui.QMenu("Plot Menu", self.plotWidget)
ct_menu.addAction(self.plotWidget.zoomAction)
ct_menu.addAction(self.plotWidget.actionAutoScale)
ct_menu.addSeparator()
ct_menu.addAction(self.plotWidget.saveCSVAction)
ct_menu.addAction(self.plotWidget.mpl2ClipAction)
ct_menu.addSeparator()
ct_menu.addAction(self.removeEICAction)
ct_menu.exec_(self.plotWidget.mapToGlobal(point))
def setupR(self):
peakTableName = 'tempPeakTable.csv'
self.peakTableName = os.path.join(self.curDir, peakTableName)
try:
ro.r('source("xcmsFuncs.R")')
except:
exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
traceback.print_exception(exceptionType, exceptionValue, exceptionTraceback, file=sys.stdout)
# print 'Error saving figure data'
errorMsg = "Sorry: %s\n\n:%s\n%s\n"%(exceptionType, exceptionValue, exceptionTraceback)
return QtGui.QMessageBox.warning(self, "R Source Error", errorMsg)
print errorMsg
#print peakTableName
def setXCMSGroup(self, xcmsSetObject, fileName = None):
if fileName != None:
if xcmsSetObject != None:
self.curXSET = xcmsSetObject
ro.r.writePeakTable(self.curXSET, fileName)
if os.path.isfile(fileName):
self.RoutputTE.append('xcms peak table written to: %s'%fileName)
else:
if xcmsSetObject != None:
self.curXSET = xcmsSetObject
ro.r.writePeakTable(self.curXSET, self.peakTableName)
if os.path.isfile(self.peakTableName):
self.RoutputTE.append('xcms peak table written to: %s'%self.peakTableName)
def saveXCMSResultsCSV(self):
if self.curXSET != None:
if os.path.isfile(self.peakTableName):
fileName = str(self.SaveCSVDialog())
if fileName != None:
self.setXCMSGroup(self.curXSET, fileName)
# #shutil.copy(self.peakTableName, fileName)
# if os.path.isfile(fileName):
# self.RoutputTE.append('xcms peak table written to: %s'%fileName)
else:
Msg = 'No XSET Exists\nTry Again!'
return QtGui.QMessageBox.warning(self, "There is no xset instance, hence no table!", Msg )
def fetchEIC(self):
if self.curXSET != None:
if self.rtTypeCB.isChecked():
rtType = "corrected"
else:
rtType = "raw"
mzlo = self.mzStartSB.value()
mzhi = self.mzStopSB.value()
if mzlo > mzhi:
Msg = 'm/z start must be lower than m/z stop!'
return QtGui.QMessageBox.warning(self, "Try Again Slick", Msg )
mzRange = ro.r.cbind(mzmin=mzlo,mzmax=mzhi)
if self.rtWidthSB_Stop.value() == -1:
usrRTrange = self.rtWidthSB.value()
else:
usrRTrange = ro.r.cbind(self.rtWidthSB.value(),self.rtWidthSB_Stop.value())
eic = ro.r.getEIC(self.curXSET, mzRange, rtrange=usrRTrange,rt=rtType)
self.eicClass.appendEIC(eic)
self.updateGUI()
self.eicIndexSB.setValue(self.eicIndexSB.maximum())
#self.RoutputTE.append('xcms peak table written to: %s'%fileName)
else:
Msg = 'No XSET Exists\nTry Again!'
return QtGui.QMessageBox.warning(self, "No xset. No EIC.", Msg )
def SaveCSVDialog(self):
fileName = QtGui.QFileDialog.getSaveFileName(self, "Select File to Save", self.curDir,"csv (*.csv)")
if not fileName.isEmpty():
print fileName
return fileName
else:
return None
def SFDialog(self):
fileName = QtGui.QFileDialog.getSaveFileName(self, "Select File to Save", self.curDir,"HDF5 Files (*.h5)")
if not fileName.isEmpty():
print fileName
return fileName
else:
return None
def LFDialog(self):
fileName = QtGui.QFileDialog.getOpenFileName(self,\
"Select File to Load",\
self.curDir, 'HDF5 File (*.h5)')
if not fileName.isEmpty():
print fileName
return fileName
else:
return None
def loadHDF52EICs(self):
#need qualifier to wipe out old one....
msgTitle = 'Overwrite existing EIC set'
overWriteStr = 'Clear current EIC and load a new set?'
if self.__askConfirm__(msgTitle,overWriteStr):
fileName = str(self.LFDialog())
if fileName != None:
self.eicClass = EIC()
t1 = time.clock()
self.eicClass.loadHDF5(fileName)
t2 = time.clock()-t1
self.RoutputTE.append('HDF5 Read Time: %.4f seconds'%t2)
self.updateGUI()
def saveEICs2HDF5(self):
fileName = str(self.SFDialog())
if fileName != None:
if self.eicClass != None:
t1 = time.clock()
self.eicClass.save2HDF5(fileName)
t2 = time.clock()-t1
self.RoutputTE.append('HDF5 Write Time: %.4f seconds'%t2)
else:
rMsg = 'No xcms Data Exists to Save'
return QtGui.QMessageBox.warning(self, "Run XCMS or Load a File!", rMsg )
def loadRPY2Batch(self):
print "Batch Button Load Clicked"
def getThreadEIC(self, eicClass):
if eicClass != None:
self.eicClass = eicClass
self.updateGUI()
def indexChanged(self, index):
if self.ignoreSignal:
return
else:
self.plotIndex = index
# print self.plotIndex
QtCore.QTimer.singleShot(750, self.plotByIndex)
def add2ROutput(self, rVector):
for item in rVector:
self.RoutputTE.append(item)
self.RoutputTE.append("\n")
def plotByIndex(self):
self.curIndex = self.plotIndex#need to do this because the slider is going from 1 and python counts from 0
self.curEIC = self.eicClass.eicTraces[self.curIndex]
self.plotEIC(self.curEIC)
def plotEIC(self, eicTrace):
self.eicPlot.cla()
curGroup = eicTrace.keys()[0]
dataList = eicTrace.values()[0]
metaDict = dataList[0]
dataDict = dataList[1]
mzlo = metaDict['mzlo']
mzhi = metaDict['mzhi']
sampNames = dataDict.keys()
for name in sampNames:
eic = dataDict[name]
xdata = eic['xdata']
ydata = eic['ydata']
self.eicPlot.plot(xdata, ydata, label = name)
if self.plotLegendCB.isChecked():
self.eicPlot.legend(axespad = 0.03, pad=0.25)
self.eicPlot.set_title('EIC from %.2f to %.2f m/z'%(mzlo, mzhi))
self.plotWidget.canvas.xtitle = 'Time (s)'
self.plotWidget.canvas.ytitle ='Arbitrary Intensity'
self.plotWidget.canvas.format_labels()
self.plotWidget.canvas.draw()
self.plotWidget.setFocus()
def updateROutput(self, StrOutput):
if len(StrOutput)>5:
self.RoutputTE.append(StrOutput)
else:
self.RoutputTE.insertPlainText(StrOutput)
self.RoutputTE.insertPlainText('\t')
def updateGUI(self):
numEICs = self.eicClass.numEICs
self.eicIndexSlider.setMaximum(numEICs-1)
self.eicIndexSB.setMaximum(numEICs-1)
self.eicIndexSB.setValue(0)
def startXCMSRun(self):
self.dirListWidget.selectAll()
fileList = self.dirListWidget.selectedItems()
maxMZ = None
if self.useRetcor_CB.isChecked():
maxMZ = self.mzMZCutoff_SB.value()
if len(fileList)>0:
self.fileList = []
for entry in fileList:
self.fileList.append(str(entry.toolTip()))#we use the tooltip as it contains the full path
if self.rtTypeCB.isChecked():
if self.rThread.updateThread(self.fileList, self.xcmsParamDict, self.rtWidthSB.value(), self.fillPeaks_CB.isChecked(), useRetcor = self.useRetcor_CB.isChecked(), maxMZ = maxMZ):
self.rThread.start()
else:
if self.rThread.updateThread(self.fileList, self.xcmsParamDict, self.rtWidthSB.value(), self.fillPeaks_CB.isChecked(), corType = 'raw', useRetcor = self.useRetcor_CB.isChecked(), maxMZ = maxMZ):
self.rThread.start()
# print fileList
print 'Start XCMS'
def testXCMS(self):
r = ro.r
a = r('cdfpath = system.file("cdf", package = "faahKO")')
cdfpath = ri.globalEnv.get("cdfpath")
r('cdffiles = list.files(cdfpath, recursive = TRUE, full.names = TRUE)')
r('cdffiles = cdffiles[1:3]')
cdffiles = ri.globalEnv.get("cdffiles")
cdfList = list(cdffiles)
maxMZ = None
if self.useRetcor_CB.isChecked():
maxMZ = self.mzMZCutoff_SB.value()
if len(cdffiles) == 0:
rMsg = 'Open R and enter the following:\nsource("http://bioconductor.org/biocLite.R")\nbiocLite("faahKO")'
return QtGui.QMessageBox.warning(self, "Error with Test Data", rMsg )
if self.rThread.updateThread(cdfList, self.xcmsParamDict, self.rtWidthSB.value(), self.fillPeaks_CB.isChecked(), useRetcor = self.useRetcor_CB.isChecked(), maxMZ = maxMZ):
self.rThread.start()
def showParamHelp(self, emitString):
curMethod = str(self.xcmsMethodCB.currentText())
xcmsSetHelp = ro.r.help("xcmsSet", htmlhelp = True)
print xcmsSetHelp
if curMethod == 'Matched Filter':
methodHelp = ro.r.help("findPeaks.matchedFilter", htmlhelp = True)
print methodHelp
elif curMethod == 'CentWave':
methodHelp = ro.r.help("findPeaks.centWave", htmlhelp = True)
print methodHelp
def _getDir_(self):
directory = QtGui.QFileDialog.getExistingDirectory(self, '', self.curDir)
directory = str(directory)
if directory != None:
self.curDir = directory
else:
self.curDir = os.getcwd()
def setupGUI(self):
self.xcmsMethodCB.addItems(self.xcmsParamDict.keys())
self.eicIndexSlider.setMaximum(0)
self.eicIndexSB.setMaximum(0)
def paramTableEntered(self, tableItem):
if self.paramTableWidget.currentColumn() == 0:
QtGui.QTableWidget
nextItem = self.paramTableWidget.item(self.paramTableWidget.currentRow(), 1)
self.paramTableWidget.editItem(nextItem)
return QtGui.QMessageBox.warning(self, "", "Don't do that Dave.")
else:
pass
def paramTableChanged(self, tableItem):
'''
This method accepts the new value for a given parameter
checkes to see if it is the same type as the original,
if not then return to the original value.
'''
if self.paramTableWidget.currentColumn() > 0:
curParam = str(self.paramTableWidget.item(tableItem.row(), 0).text())
curType = self.curTypeDict[curParam]
try:
tempVal = curType(str(tableItem.text()))
except:
origVal = self.curParamDict[curParam]
tableItem.setText(str(origVal))
tempVal = curType(str(tableItem.text()))
self.curParamDict[curParam] = tempVal
print self.curParamDict
def updateParamTable(self, selectText):
self.curParamDict = self.xcmsParamDict[str(selectText)]
self.curTypeDict = self.xcmsTypeDict[str(selectText)]
curParams = self.curParamDict.items()
curParams.sort()
self.paramTableWidget.clear()
self.paramTableWidget.addData(curParams)
def initFileList(self):
if not self.firstLoad:
#reinitialize GUI and spectrumList
#need to reset GUI
print "Need to reset GUI"
# self.setupGUI()
self._getDir_()
dirList, startDir = FP.Load_mzXML_Folder(self.curDir)
if startDir != None:
if os.path.exists(startDir):
self.curDir = startDir
self.curFolderLE.setText(self.curDir)
self.eicCurFolderLE.setText(self.curDir)
# print startDir
if len(dirList) !=0:
self.dirList = dirList
self.loadOk = True
self.firstLoad = False
self.addFiles()
# self.dirListWidget.addItems(self.dirList)
# if self.readThread.updateThread(dirList, loadmzXML = True):
# self.readThread.start()
elif startDir != None:
return QtGui.QMessageBox.warning(self, "No Data Found", "Check selected folder, does it have any data?")
def addFiles(self):
self.dirListWidget.clear()
for item in self.dirList:
#####Text Color Handler
if self.colorIndex%len(COLORS) == 0:
self.colorIndex = 0
self.txtColor = COLORS[self.colorIndex]
self.colorIndex +=1
else:
self.txtColor = COLORS[self.colorIndex]
self.colorIndex +=1
fileName = os.path.basename(item)
tempItem = QtGui.QListWidgetItem(fileName)
tempColor = QtGui.QColor(self.txtColor)
tempItem.setTextColor(tempColor)
tempItem.setToolTip(item)
#self.specListWidget.addItem(loadedItem.name)
self.dirListWidget.addItem(tempItem)
def __askConfirm__(self,title,message):
clickedButton = QtGui.QMessageBox.question(self,\
title,message,\
QtGui.QMessageBox.Yes,QtGui.QMessageBox.Cancel)
if clickedButton == QtGui.QMessageBox.Yes: return True
return False
def closeEvent(self, event = None):
try:
ri.endr()
except:
pass
##########Begin Ashoka Progress Bar Code....
def layoutStatusBar(self):
self.progressBar = QtGui.QProgressBar()
self.statusLabel = QtGui.QLabel("Ready")
# self.statusLabel.setMinimumSize(self.statusLabel.sizeHint())
self.statusLabel.setAlignment(QtCore.Qt.AlignLeft)
self.statusLabel.setText("Ready")
self.statusbar.addPermanentWidget(self.statusLabel)
self.progressBar.setTextVisible(False)
self.progressBar.setRange(0,100)
self.progressBar.setValue(0)
self.progressBar.setFixedHeight(15)
self.progressBar.setFixedWidth(100)
self.toggleProgressBar(False)
self.statusbar.addWidget(self.progressBar)
def resetProgressBar(self):
self.setProgressValue(0)
self.toggleProgressBar(False)
def setStatusLabel(self, text):
self.statusLabel.setText(text)
def showStatusMessage(self, text, stime):
self.statusBar().showMessage(text, stime)
def setProgressValue(self, val):
self.progressBar.setValue(val)
def toggleProgressBar(self, toggle):
self.progressBar.setVisible(toggle)
def threadProgress(self, progVal):
self.setStatusLabel("Fitting Peaks, %d segments completed." % progVal)
newVal = int(100*(progVal/self.progressMax))
self.setProgressValue(newVal)
# self.AddMessage2Tab(" %d Iterations Done." % progVal)
# print progVal, newVal, self.progressMax
def PCTProgress(self, updateString):
self.setStatusLabel(updateString)
class pyXCMSWindow(QtGui.QMainWindow, ui_main.Ui_MainWindow):
def __init__(self, parent=None):
super(pyXCMSWindow, self).__init__(parent)
self.ui = self.setupUi(self)
self.__initVars()
self.__initConnections()
self._setContext_()
self.setupGUI()
self.setupR()
def __initVars(self):
self.firstLoad = True
self.colorIndex = 0
self.txtColor = None
self.curDir = os.getcwd()
self.peakTableName = None
self.curParamDict = None
self.curTypeDict = None
self.fileList = None
# self.Rliblist = ['xcms']
# self.Rlibs = initRlibs(self.Rliblist)
self.xcmsOK = False
self.eicPlot = self.plotWidget.canvas.axDict['ax1']
self.eicList = []
self.eicDict = None
self.eicClass = None
self.curXSET = None
self.plotIndex = 0
self.initIndex = 0
self.ignoreSignal = False
self.highlighter = PH(self.batchScriptTE.document())
self.rThread = XCMSThread(self)
# self.rProcess = QtCore.QProcess()
'''
findPeaks.matchedFilter(object, fwhm = 30, sigma = fwhm/2.3548, max = 5,
snthresh = 10, step = 0.1, steps = 2, mzdiff = 0.8 - step*steps,
index = FALSE, sleep = 0)
object --xcmsRaw object
fwhm --full width at half maximum of matched filtration gaussian model peak
sigma --standard deviation of matched filtration model peak
max --maximum number of peaks per extracted ion chromatogram
snthresh --signal to noise ratio cutoff
step --step size to use for profile generation
steps --number of steps to merge prior to filtration
mzdiff --minimum difference in m/z for peaks with overlapping retention times
index --return indicies instead of values for m/z and retention times
sleep --number of seconds to pause between plotting peak finding cycles
'''
self.matchedFilterParams = {
'fwhm': 30.,
'sigma': 30 / 2.3548,
'max': 5.,
'snthresh': 10.,
'step': 0.01,
'steps': 2.,
'mzdiff': 0.01,
}
self.matchedFilterTypes = {
'fwhm': float,
'sigma': float,
'max': float,
'snthresh': float,
'step': float,
'steps': float,
'mzdiff': float
}
##########################
'''
CentWave
object = "xcmsRaw"
findPeaks.centWave(object, ppm=25, peakwidth=c(20,50),
snthresh=10, prefilter=c(3,100), integrate=1, mzdiff=-0.001,
fitgauss=FALSE, scanrange= numeric(), sleep=0, verbose.columns=FALSE)
object --xcmsSet objectprint methodHelp
ppm --maxmial tolerated m/z deviation in consecutive scans, in ppm (parts per million)
peakwidth --Chromatographic peak width, given as range (min,max) in seconds
snthresh --signal to noise ratio cutoff, definition see below.
prefilter --prefilter=c(k,I). Prefilter step for the first phase. Mass traces are only retained if they contain at least k peaks with intensity >= I.
integrate --Integration method. If =1 peak limits are found through descent on the mexican hat filtered data, if =2 the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.
mzdiff --minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap
fitgauss --logical, if TRUE a Gaussian is fitted to each peak
scanrange --scan range to process
sleep --number of seconds to pause between plotting peak finding cycles
verbose.columns logical, if TRUE additional peak meta data columns are returned
'''
#this method is not working well yet for the ORBITRAP DATA ACQUIRED AT PNNL
self.centWaveParams = {
'ppm': 10.,
'peakwidth': str(
[20, 50]
), #this needs to be fixed, the new version of PyQt4 handles this better
'snthresh': 10.,
'prefilter': str([3, 100]),
'mzdiff': -0.001,
}
self.centWaveTypes = {
'ppm': float,
'peakwidth': str,
'snthresh': float,
'prefilter': str,
'mzdiff': float,
}
################################
self.groupParams = {'bw': 30., 'minfrac': 0.1, 'mzwid': 0.1, 'max': 3}
self.groupTypes = {
'bw': float,
'minfrac': float,
'mzwid': float,
'max': int
}
##############################
self.retcorParams = {
'extra': 2,
'span': 0.5,
'f': 'symmetric',
'plottype': 'none',
'missing': 2
}
self.retcorTypes = {
'extra': int,
'span': float,
'f': str,
'plottype': str,
'missing': str
}
#########################
self.xcmsParamDict = {
'Matched Filter': self.matchedFilterParams,
'Group Params': self.groupParams,
'Retcor Params': self.retcorParams,
'CentWave': self.centWaveParams
}
self.xcmsTypeDict = {
'Matched Filter': self.matchedFilterTypes,
'Group Params': self.groupTypes,
'Retcor Params': self.retcorTypes,
'CentWave': self.centWaveTypes
}
def __initConnections(self):
QtCore.QObject.connect(self.getFolderBtn, QtCore.SIGNAL("clicked()"),
self.initFileList)
QtCore.QObject.connect(self.xcmsMethodCB,
QtCore.SIGNAL("currentIndexChanged(QString)"),
self.updateParamTable)
QtCore.QObject.connect(
self.paramTableWidget,
QtCore.SIGNAL("itemDoubleClicked(QTableWidgetItem*)"),
self.paramTableEntered)
QtCore.QObject.connect(self.paramTableWidget,
QtCore.SIGNAL("itemChanged(QTableWidgetItem*)"),
self.paramTableChanged)
QtCore.QObject.connect(self.paramTableWidget,
QtCore.SIGNAL("helpRequested(PyQt_PyObject)"),
self.showParamHelp)
QtCore.QObject.connect(self.actionTest_XCMS,
QtCore.SIGNAL("triggered()"), self.testXCMS)
QtCore.QObject.connect(self.actionSave_HDF5,
QtCore.SIGNAL("triggered()"),
self.saveEICs2HDF5)
QtCore.QObject.connect(self.actionLoad_HDF5,
QtCore.SIGNAL("triggered()"),
self.loadHDF52EICs)
QtCore.QObject.connect(self.actionSave_Results_Table,
QtCore.SIGNAL("triggered()"),
self.saveXCMSResultsCSV)
QtCore.QObject.connect(self.getEICBtn, QtCore.SIGNAL("clicked()"),
self.fetchEIC)
QtCore.QObject.connect(self.runXCMSBtn, QtCore.SIGNAL("clicked()"),
self.startXCMSRun)
QtCore.QObject.connect(self.loadRPY2BatchBtn,
QtCore.SIGNAL("clicked()"), self.loadRPY2Batch)
QtCore.QObject.connect(self.eicIndexSB,
QtCore.SIGNAL("valueChanged(int)"),
self.indexChanged)
QtCore.QObject.connect(self.rThread,
QtCore.SIGNAL("xcmsOutUpdate(PyQt_PyObject)"),
self.updateROutput)
QtCore.QObject.connect(self.rThread,
QtCore.SIGNAL("xcmsGetEIC(PyQt_PyObject)"),
self.getThreadEIC)
QtCore.QObject.connect(self.rThread,
QtCore.SIGNAL("xcmsSet(PyQt_PyObject)"),
self.setXCMSGroup)
self.removeFileAction = QtGui.QAction("Remove File", self)
self.dirListWidget.addAction(self.removeFileAction)
QtCore.QObject.connect(self.removeFileAction,
QtCore.SIGNAL("triggered()"), self.removeFile)
self.removeEICAction = QtGui.QAction("Remove EIC", self)
self.plotWidget.addAction(self.removeEICAction)
QtCore.QObject.connect(self.removeEICAction,
QtCore.SIGNAL("triggered()"), self.removeEIC)
def removeEIC(self):
print "Remove EIC"
self.curIndex = self.plotIndex #need to do this because the slider is going from 1 and python counts from 0
self.eicClass.eicTraces.pop(self.curIndex)
self.eicClass.numEICs = self.eicClass.numEICs - 1
numEICs = self.eicClass.numEICs
self.eicIndexSlider.setMaximum(numEICs - 1)
self.eicIndexSB.setMaximum(numEICs - 1)
self.eicIndexSB.setValue(self.curIndex - 1) #just to be safe
def removeFile(self):
selItem = self.dirListWidget.selectedItems()[0]
curRow = self.dirListWidget.row(selItem)
print curRow
self.dirListWidget.takeItem(curRow)
self.dirList.pop(curRow)
print len(self.dirList)
def _setContext_(self):
self.plotWidget.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.plotWidget.connect(
self.plotWidget,
QtCore.SIGNAL("customContextMenuRequested(QPoint)"),
self._plotContext_)
self.dirListWidget.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.dirListWidget.connect(
self.dirListWidget,
QtCore.SIGNAL("customContextMenuRequested(QPoint)"),
self._dirListContext_)
def _dirListContext_(self, point):
ct_menu = QtGui.QMenu("File List Menu", self.dirListWidget)
ct_menu.addAction(self.removeFileAction)
ct_menu.exec_(self.dirListWidget.mapToGlobal(point))
def _plotContext_(self, point):
ct_menu = QtGui.QMenu("Plot Menu", self.plotWidget)
ct_menu.addAction(self.plotWidget.zoomAction)
ct_menu.addAction(self.plotWidget.actionAutoScale)
ct_menu.addSeparator()
ct_menu.addAction(self.plotWidget.saveCSVAction)
ct_menu.addAction(self.plotWidget.mpl2ClipAction)
ct_menu.addSeparator()
ct_menu.addAction(self.removeEICAction)
ct_menu.exec_(self.plotWidget.mapToGlobal(point))
def setupR(self):
peakTableName = 'tempPeakTable.csv'
self.peakTableName = os.path.join(self.curDir, peakTableName)
try:
ro.r('source("xcmsFuncs.R")')
except:
exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
traceback.print_exception(exceptionType,
exceptionValue,
exceptionTraceback,
file=sys.stdout)
# print 'Error saving figure data'
errorMsg = "Sorry: %s\n\n:%s\n%s\n" % (
exceptionType, exceptionValue, exceptionTraceback)
return QtGui.QMessageBox.warning(self, "R Source Error", errorMsg)
print errorMsg
#print peakTableName
def setXCMSGroup(self, xcmsSetObject, fileName=None):
if fileName != None:
if xcmsSetObject != None:
self.curXSET = xcmsSetObject
ro.r.writePeakTable(self.curXSET, fileName)
if os.path.isfile(fileName):
self.RoutputTE.append('xcms peak table written to: %s' %
fileName)
else:
if xcmsSetObject != None:
self.curXSET = xcmsSetObject
ro.r.writePeakTable(self.curXSET, self.peakTableName)
if os.path.isfile(self.peakTableName):
self.RoutputTE.append('xcms peak table written to: %s' %
self.peakTableName)
def saveXCMSResultsCSV(self):
if self.curXSET != None:
if os.path.isfile(self.peakTableName):
fileName = str(self.SaveCSVDialog())
if fileName != None:
self.setXCMSGroup(self.curXSET, fileName)
# #shutil.copy(self.peakTableName, fileName)
# if os.path.isfile(fileName):
# self.RoutputTE.append('xcms peak table written to: %s'%fileName)
else:
Msg = 'No XSET Exists\nTry Again!'
return QtGui.QMessageBox.warning(
self, "There is no xset instance, hence no table!", Msg)
def fetchEIC(self):
if self.curXSET != None:
if self.rtTypeCB.isChecked():
rtType = "corrected"
else:
rtType = "raw"
mzlo = self.mzStartSB.value()
mzhi = self.mzStopSB.value()
if mzlo > mzhi:
Msg = 'm/z start must be lower than m/z stop!'
return QtGui.QMessageBox.warning(self, "Try Again Slick", Msg)
mzRange = ro.r.cbind(mzmin=mzlo, mzmax=mzhi)
if self.rtWidthSB_Stop.value() == -1:
usrRTrange = self.rtWidthSB.value()
else:
usrRTrange = ro.r.cbind(self.rtWidthSB.value(),
self.rtWidthSB_Stop.value())
eic = ro.r.getEIC(self.curXSET,
mzRange,
rtrange=usrRTrange,
rt=rtType)
self.eicClass.appendEIC(eic)
self.updateGUI()
self.eicIndexSB.setValue(self.eicIndexSB.maximum())
#self.RoutputTE.append('xcms peak table written to: %s'%fileName)
else:
Msg = 'No XSET Exists\nTry Again!'
return QtGui.QMessageBox.warning(self, "No xset. No EIC.", Msg)
def SaveCSVDialog(self):
fileName = QtGui.QFileDialog.getSaveFileName(self,
"Select File to Save",
self.curDir,
"csv (*.csv)")
if not fileName.isEmpty():
print fileName
return fileName
else:
return None
def SFDialog(self):
fileName = QtGui.QFileDialog.getSaveFileName(self,
"Select File to Save",
self.curDir,
"HDF5 Files (*.h5)")
if not fileName.isEmpty():
print fileName
return fileName
else:
return None
def LFDialog(self):
fileName = QtGui.QFileDialog.getOpenFileName(self,\
"Select File to Load",\
self.curDir, 'HDF5 File (*.h5)')
if not fileName.isEmpty():
print fileName
return fileName
else:
return None
def loadHDF52EICs(self):
#need qualifier to wipe out old one....
msgTitle = 'Overwrite existing EIC set'
overWriteStr = 'Clear current EIC and load a new set?'
if self.__askConfirm__(msgTitle, overWriteStr):
fileName = str(self.LFDialog())
if fileName != None:
self.eicClass = EIC()
t1 = time.clock()
self.eicClass.loadHDF5(fileName)
t2 = time.clock() - t1
self.RoutputTE.append('HDF5 Read Time: %.4f seconds' % t2)
self.updateGUI()
def saveEICs2HDF5(self):
fileName = str(self.SFDialog())
if fileName != None:
if self.eicClass != None:
t1 = time.clock()
self.eicClass.save2HDF5(fileName)
t2 = time.clock() - t1
self.RoutputTE.append('HDF5 Write Time: %.4f seconds' % t2)
else:
rMsg = 'No xcms Data Exists to Save'
return QtGui.QMessageBox.warning(self,
"Run XCMS or Load a File!",
rMsg)
def loadRPY2Batch(self):
print "Batch Button Load Clicked"
def getThreadEIC(self, eicClass):
if eicClass != None:
self.eicClass = eicClass
self.updateGUI()
def indexChanged(self, index):
if self.ignoreSignal:
return
else:
self.plotIndex = index
# print self.plotIndex
QtCore.QTimer.singleShot(750, self.plotByIndex)
def add2ROutput(self, rVector):
for item in rVector:
self.RoutputTE.append(item)
self.RoutputTE.append("\n")
def plotByIndex(self):
self.curIndex = self.plotIndex #need to do this because the slider is going from 1 and python counts from 0
self.curEIC = self.eicClass.eicTraces[self.curIndex]
self.plotEIC(self.curEIC)
def plotEIC(self, eicTrace):
self.eicPlot.cla()
curGroup = eicTrace.keys()[0]
dataList = eicTrace.values()[0]
metaDict = dataList[0]
dataDict = dataList[1]
mzlo = metaDict['mzlo']
mzhi = metaDict['mzhi']
sampNames = dataDict.keys()
for name in sampNames:
eic = dataDict[name]
xdata = eic['xdata']
ydata = eic['ydata']
self.eicPlot.plot(xdata, ydata, label=name)
if self.plotLegendCB.isChecked():
self.eicPlot.legend(axespad=0.03, pad=0.25)
self.eicPlot.set_title('EIC from %.2f to %.2f m/z' % (mzlo, mzhi))
self.plotWidget.canvas.xtitle = 'Time (s)'
self.plotWidget.canvas.ytitle = 'Arbitrary Intensity'
self.plotWidget.canvas.format_labels()
self.plotWidget.canvas.draw()
self.plotWidget.setFocus()
def updateROutput(self, StrOutput):
if len(StrOutput) > 5:
self.RoutputTE.append(StrOutput)
else:
self.RoutputTE.insertPlainText(StrOutput)
self.RoutputTE.insertPlainText('\t')
def updateGUI(self):
numEICs = self.eicClass.numEICs
self.eicIndexSlider.setMaximum(numEICs - 1)
self.eicIndexSB.setMaximum(numEICs - 1)
self.eicIndexSB.setValue(0)
def startXCMSRun(self):
self.dirListWidget.selectAll()
fileList = self.dirListWidget.selectedItems()
maxMZ = None
if self.useRetcor_CB.isChecked():
maxMZ = self.mzMZCutoff_SB.value()
if len(fileList) > 0:
self.fileList = []
for entry in fileList:
self.fileList.append(str(entry.toolTip(
))) #we use the tooltip as it contains the full path
if self.rtTypeCB.isChecked():
if self.rThread.updateThread(
self.fileList,
self.xcmsParamDict,
self.rtWidthSB.value(),
self.fillPeaks_CB.isChecked(),
useRetcor=self.useRetcor_CB.isChecked(),
maxMZ=maxMZ):
self.rThread.start()
else:
if self.rThread.updateThread(
self.fileList,
self.xcmsParamDict,
self.rtWidthSB.value(),
self.fillPeaks_CB.isChecked(),
corType='raw',
useRetcor=self.useRetcor_CB.isChecked(),
maxMZ=maxMZ):
self.rThread.start()
# print fileList
print 'Start XCMS'
def testXCMS(self):
r = ro.r
a = r('cdfpath = system.file("cdf", package = "faahKO")')
cdfpath = ri.globalEnv.get("cdfpath")
r('cdffiles = list.files(cdfpath, recursive = TRUE, full.names = TRUE)'
)
r('cdffiles = cdffiles[1:3]')
cdffiles = ri.globalEnv.get("cdffiles")
cdfList = list(cdffiles)
maxMZ = None
if self.useRetcor_CB.isChecked():
maxMZ = self.mzMZCutoff_SB.value()
if len(cdffiles) == 0:
rMsg = 'Open R and enter the following:\nsource("http://bioconductor.org/biocLite.R")\nbiocLite("faahKO")'
return QtGui.QMessageBox.warning(self, "Error with Test Data",
rMsg)
if self.rThread.updateThread(cdfList,
self.xcmsParamDict,
self.rtWidthSB.value(),
self.fillPeaks_CB.isChecked(),
useRetcor=self.useRetcor_CB.isChecked(),
maxMZ=maxMZ):
self.rThread.start()
def showParamHelp(self, emitString):
curMethod = str(self.xcmsMethodCB.currentText())
xcmsSetHelp = ro.r.help("xcmsSet", htmlhelp=True)
print xcmsSetHelp
if curMethod == 'Matched Filter':
methodHelp = ro.r.help("findPeaks.matchedFilter", htmlhelp=True)
print methodHelp
elif curMethod == 'CentWave':
methodHelp = ro.r.help("findPeaks.centWave", htmlhelp=True)
print methodHelp
def _getDir_(self):
directory = QtGui.QFileDialog.getExistingDirectory(
self, '', self.curDir)
directory = str(directory)
if directory != None:
self.curDir = directory
else:
self.curDir = os.getcwd()
def setupGUI(self):
self.xcmsMethodCB.addItems(self.xcmsParamDict.keys())
self.eicIndexSlider.setMaximum(0)
self.eicIndexSB.setMaximum(0)
def paramTableEntered(self, tableItem):
if self.paramTableWidget.currentColumn() == 0:
QtGui.QTableWidget
nextItem = self.paramTableWidget.item(
self.paramTableWidget.currentRow(), 1)
self.paramTableWidget.editItem(nextItem)
return QtGui.QMessageBox.warning(self, "", "Don't do that Dave.")
else:
pass
def paramTableChanged(self, tableItem):
'''
This method accepts the new value for a given parameter
checkes to see if it is the same type as the original,
if not then return to the original value.
'''
if self.paramTableWidget.currentColumn() > 0:
curParam = str(
self.paramTableWidget.item(tableItem.row(), 0).text())
curType = self.curTypeDict[curParam]
try:
tempVal = curType(str(tableItem.text()))
except:
origVal = self.curParamDict[curParam]
tableItem.setText(str(origVal))
tempVal = curType(str(tableItem.text()))
self.curParamDict[curParam] = tempVal
print self.curParamDict
def updateParamTable(self, selectText):
self.curParamDict = self.xcmsParamDict[str(selectText)]
self.curTypeDict = self.xcmsTypeDict[str(selectText)]
curParams = self.curParamDict.items()
curParams.sort()
self.paramTableWidget.clear()
self.paramTableWidget.addData(curParams)
def initFileList(self):
if not self.firstLoad:
#reinitialize GUI and spectrumList
#need to reset GUI
print "Need to reset GUI"
# self.setupGUI()
self._getDir_()
dirList, startDir = FP.Load_mzXML_Folder(self.curDir)
if startDir != None:
if os.path.exists(startDir):
self.curDir = startDir
self.curFolderLE.setText(self.curDir)
self.eicCurFolderLE.setText(self.curDir)
# print startDir
if len(dirList) != 0:
self.dirList = dirList
self.loadOk = True
self.firstLoad = False
self.addFiles()
# self.dirListWidget.addItems(self.dirList)
# if self.readThread.updateThread(dirList, loadmzXML = True):
# self.readThread.start()
elif startDir != None:
return QtGui.QMessageBox.warning(
self, "No Data Found",
"Check selected folder, does it have any data?")
def addFiles(self):
self.dirListWidget.clear()
for item in self.dirList:
#####Text Color Handler
if self.colorIndex % len(COLORS) == 0:
self.colorIndex = 0
self.txtColor = COLORS[self.colorIndex]
self.colorIndex += 1
else:
self.txtColor = COLORS[self.colorIndex]
self.colorIndex += 1
fileName = os.path.basename(item)
tempItem = QtGui.QListWidgetItem(fileName)
tempColor = QtGui.QColor(self.txtColor)
tempItem.setTextColor(tempColor)
tempItem.setToolTip(item)
#self.specListWidget.addItem(loadedItem.name)
self.dirListWidget.addItem(tempItem)
def __askConfirm__(self, title, message):
clickedButton = QtGui.QMessageBox.question(self,\
title,message,\
QtGui.QMessageBox.Yes,QtGui.QMessageBox.Cancel)
if clickedButton == QtGui.QMessageBox.Yes: return True
return False
def closeEvent(self, event=None):
try:
ri.endr()
except:
pass
##########Begin Ashoka Progress Bar Code....
def layoutStatusBar(self):
self.progressBar = QtGui.QProgressBar()
self.statusLabel = QtGui.QLabel("Ready")
# self.statusLabel.setMinimumSize(self.statusLabel.sizeHint())
self.statusLabel.setAlignment(QtCore.Qt.AlignLeft)
self.statusLabel.setText("Ready")
self.statusbar.addPermanentWidget(self.statusLabel)
self.progressBar.setTextVisible(False)
self.progressBar.setRange(0, 100)
self.progressBar.setValue(0)
self.progressBar.setFixedHeight(15)
self.progressBar.setFixedWidth(100)
self.toggleProgressBar(False)
self.statusbar.addWidget(self.progressBar)
def resetProgressBar(self):
self.setProgressValue(0)
self.toggleProgressBar(False)
def setStatusLabel(self, text):
self.statusLabel.setText(text)
def showStatusMessage(self, text, stime):
self.statusBar().showMessage(text, stime)
def setProgressValue(self, val):
self.progressBar.setValue(val)
def toggleProgressBar(self, toggle):
self.progressBar.setVisible(toggle)
def threadProgress(self, progVal):
self.setStatusLabel("Fitting Peaks, %d segments completed." % progVal)
newVal = int(100 * (progVal / self.progressMax))
self.setProgressValue(newVal)
# self.AddMessage2Tab(" %d Iterations Done." % progVal)
# print progVal, newVal, self.progressMax
def PCTProgress(self, updateString):
self.setStatusLabel(updateString)