def generateSpeciesSlicesFwhm(self,
speciesName,
leftMultiplier=1,
rightMultiplier=1):
"""Create data slices using peak width from mass spectrum fit
for a specific species.
:parameter speciesName: Name of molecular species
:parameter leftMultiplier: Value to multiply the peak fwhm below the mean
:parameter rightMultiplier: Value to multiply the peak fwhm above the mean
"""
self.dataSlices[speciesName] = collections.OrderedDict()
self.generateMassSpectrum()
left = float(leftMultiplier * self.species[speciesName].peakFwhm) / 2
right = float(rightMultiplier * self.species[speciesName].peakFwhm) / 2
for z in self.species[speciesName].charges:
mz = self.species[speciesName].getMz(z)
mzIndex = utils.closest(mz, self.xaxis)
mzIndex = localMaxima(mzIndex,
self.massSpectrum.xvals,
self.massSpectrum.yvals,
scan_range=10)
leftI = utils.closest(mz - left, self.xaxis)
rightI = utils.closest(mz + right, self.xaxis)
self.dataSlices[speciesName][z] = self._generateSlice(
[leftI, rightI])
self.dataSlices[speciesName][z].generateAtd()
self.dataSlices[speciesName][z].charge = z
def limitAxisX(self, lims):
"""Reduce the range of values in the dataset. Reducing the xlimits here
automatically reduces the yaxis.
:parameter lims: List of limits in the form [lower,upper]
"""
lowerI = utils.closest(lims[0], self.xvals)
higherI = utils.closest(lims[1], self.xvals)
self.xvals = self.xvals[lowerI:higherI]
self.yvals = self.yvals[lowerI:higherI]
self.rawyvals = self.rawyvals[lowerI:higherI]
def eventButtonTogglePeakPicking(self, event): # wxGlade: AtroposGui.<event_handler>
"""This function just activates the peak picking so that the on_pick() function
is able to record mouse clicks.
When the toggle is turned off then the value is registered.
"""
if self.buttonTogglePeakPicking.GetValue() == True:
self.msPanel.pickingActive = True
self.msPanel.axMs.set_picker(True)
self.msPanel.pickedPeakIdLimit -= 1
elif self.buttonTogglePeakPicking.GetValue() == False:
self.msPanel.pickingActive = False
self.msPanel.pickedAlready = False
if self.msPanel.pickedValue:
peakId = self.msPanel.pickedPeakIdLimit
yi = utils.closest(self.msPanel.pickedValue, self.msPanel.ms.xvals)
y = self.msPanel.ms.yvals[yi]
self.msPanel.ms.gPeaks[peakId] = [self.msPanel.pickedValue,y]
self.settings.addPeakMz(self.msPanel.pickedValue)
else:
self.msPanel.pickedPeakIdLimit += 1
self.msPanel.pickedValue = None
def getAtdsFromMzLims(self, mzLow, mzHigh):
"""Extract arrival times from mass spectrum limits.
:parameter mzLow: Lower limit for extraction
:parameter mzHigh: Upper limit for extraction
:returns: Dictionary of imClasses.Atd() objects (d[filename] = Atd())
"""
atds = OrderedDict()
for fn, imOb in self.settings.loadedFiles.items():
mzLowIndex = utils.closest(mzLow,
self.settings.massSpectra[fn].xvals)
mzHighIndex = utils.closest(mzHigh,
self.settings.massSpectra[fn].xvals)
ds = imOb._generateSlice([mzLowIndex, mzHighIndex])
ds.generateAtd()
atds[fn] = ds.atd
return atds
def _getMatrixWithinLimits(self):
"""Applies the self.xlims and self.ylims limits and returns the reduced
matrix with x and y axes.
:returns: matrix, x axis, yaxis
"""
lowIndexX = utils.closest(self.xlims[0], self.xaxis)
highIndexX = utils.closest(self.xlims[1], self.xaxis)
x = self.xaxis[lowIndexX:highIndexX]
lowIndexY = utils.closest(self.ylims[0], self.yaxis)
highIndexY = utils.closest(self.ylims[1], self.yaxis)
y = self.yaxis[lowIndexY:highIndexY]
matrix = self.matrix[lowIndexY:highIndexY,lowIndexX:highIndexX]
return matrix, x, y
def _getMatrixWithinLimits(self):
"""Applies the self.xlims and self.ylims limits and returns the reduced
matrix with x and y axes.
:returns: matrix, x axis, yaxis
"""
lowIndexX = utils.closest(self.xlims[0], self.xaxis)
highIndexX = utils.closest(self.xlims[1], self.xaxis)
x = self.xaxis[lowIndexX:highIndexX]
lowIndexY = utils.closest(self.ylims[0], self.yaxis)
highIndexY = utils.closest(self.ylims[1], self.yaxis)
y = self.yaxis[lowIndexY:highIndexY]
matrix = self.matrix[lowIndexY:highIndexY, lowIndexX:highIndexX]
return matrix, x, y
def eventButtonTogglePeakPicking(
self, event): # wxGlade: AtroposGui.<event_handler>
"""This function just activates the peak picking so that the on_pick() function
is able to record mouse clicks.
When the toggle is turned off then the value is registered.
"""
if self.buttonTogglePeakPicking.GetValue() == True:
self.msPanel.pickingActive = True
self.msPanel.axMs.set_picker(True)
self.msPanel.pickedPeakIdLimit -= 1
elif self.buttonTogglePeakPicking.GetValue() == False:
self.msPanel.pickingActive = False
self.msPanel.pickedAlready = False
if self.msPanel.pickedValue:
peakId = self.msPanel.pickedPeakIdLimit
yi = utils.closest(self.msPanel.pickedValue,
self.msPanel.ms.xvals)
y = self.msPanel.ms.yvals[yi]
self.msPanel.ms.gPeaks[peakId] = [self.msPanel.pickedValue, y]
self.settings.addPeakMz(self.msPanel.pickedValue)
else:
self.msPanel.pickedPeakIdLimit += 1
self.msPanel.pickedValue = None
def plotConformationHeights(self,ax):
"""Track the abundance of the different conformations across
the data files and plot them.
"""
# gather the data
ccsAxes,ccsLines = self.settings.getCcsLines()
ccsDic = OrderedDict()
for ccs in self.settings.conformations:
ccsDic[ccs] = []
for xaxis,line in zip(ccsAxes,ccsLines):
height = line[utils.closest(xaxis,ccs)]
ccsDic[ccs].append(height)
# plot it
if not '' in self.settings.values and len(self.settings.values):
valueList = self.settings.values
ax.set_xlabel(self.settings.units)
else:
valueList = [ x for x in range(len(ccsDic.keys())) ]
ax.set_xlabel('Arbitary progression')
ax.set_xticks(valueList)
for i,ccs in enumerate(ccsDic.keys()):
ax.plot(valueList, ccsDic[ccs], label=str(ccs),color=utils.colourList[i])
def getTotalIntensity(self,xvals,yvals):
"""Using the supplied data, sum the intensity of the highest
point of the data at the m/z value for each charge state in
self.charges using self.mass as the mass.
"""
'''Gets experimental intensity'''
intensity = 0
for charge in self.charges:
mz = utils.get_mz(self.mass, charge)
i = utils.closest(mz, xvals)
intensity += yvals[i]
return intensity
def generateSpeciesSlicesFwhm(self,speciesName,leftMultiplier=1,rightMultiplier=1):
"""Create data slices using peak width from mass spectrum fit
for a specific species.
:parameter speciesName: Name of molecular species
:parameter leftMultiplier: Value to multiply the peak fwhm below the mean
:parameter rightMultiplier: Value to multiply the peak fwhm above the mean
"""
self.dataSlices[speciesName] = collections.OrderedDict()
self.generateMassSpectrum()
left = float(leftMultiplier*self.species[speciesName].peakFwhm)/2
right = float(rightMultiplier*self.species[speciesName].peakFwhm)/2
for z in self.species[speciesName].charges:
mz = self.species[speciesName].getMz(z)
mzIndex = utils.closest(mz,self.xaxis)
mzIndex = localMaxima(mzIndex,self.massSpectrum.xvals,self.massSpectrum.yvals, scan_range=10)
leftI = utils.closest(mz-left,self.xaxis)
rightI = utils.closest(mz+right,self.xaxis)
self.dataSlices[speciesName][z] = self._generateSlice([leftI,rightI])
self.dataSlices[speciesName][z].generateAtd()
self.dataSlices[speciesName][z].charge = z
def getTotalIntensity(self, xvals, yvals):
"""Using the supplied data, sum the intensity of the highest
point of the data at the m/z value for each charge state in
self.charges using self.mass as the mass.
"""
'''Gets experimental intensity'''
intensity = 0
for charge in self.charges:
mz = utils.get_mz(self.mass, charge)
i = utils.closest(mz, xvals)
intensity += yvals[i]
return intensity
def generateSpeciesSlicesExplicit(self,limitDic):
"""Create data slices using explicit m/z limits for arrival
time data extraction, for all supplied species and charge states.
:parameter limitDic: d[species][z] = [lowerLimit,upperLimit]
"""
'''
limitDic generated by ChargeStatePeak.py
Has actual absolute mz values for the limits
Does all species at the same time unlike self.generateSpeciesSlicesFwhm()
which does them all together
limitDic structure is species>z>[lowerMz,upperMz]
'''
self.generateMassSpectrum()
for speciesName,subD in limitDic.items():
self.dataSlices[speciesName] = collections.OrderedDict()
for z,limit in subD.items():
leftI = utils.closest(limit[0],self.xaxis)
rightI = utils.closest(limit[-1],self.xaxis)
self.dataSlices[speciesName][z] = self._generateSlice([leftI,rightI])
self.dataSlices[speciesName][z].generateAtd()
self.dataSlices[speciesName][z].charge = z
def generateSpeciesSlicesExplicit(self, limitDic):
"""Create data slices using explicit m/z limits for arrival
time data extraction, for all supplied species and charge states.
:parameter limitDic: d[species][z] = [lowerLimit,upperLimit]
"""
'''
limitDic generated by ChargeStatePeak.py
Has actual absolute mz values for the limits
Does all species at the same time unlike self.generateSpeciesSlicesFwhm()
which does them all together
limitDic structure is species>z>[lowerMz,upperMz]
'''
self.generateMassSpectrum()
for speciesName, subD in limitDic.items():
self.dataSlices[speciesName] = collections.OrderedDict()
for z, limit in subD.items():
leftI = utils.closest(limit[0], self.xaxis)
rightI = utils.closest(limit[-1], self.xaxis)
self.dataSlices[speciesName][z] = self._generateSlice(
[leftI, rightI])
self.dataSlices[speciesName][z].generateAtd()
self.dataSlices[speciesName][z].charge = z
def addPeak(self, mz):
"""This function allows you to add additional peaks not found using the
findPeaks method"""
try:
keys = sorted(self.gPeaks.keys())
id = 1 + keys[-1]
self.gPeaks[id] = {}
except:
id = 0
self.gPeaks = {}
self.gPeaks[id] = {}
self.gPeaks[id] = [[], []]
self.gPeaks[id][0] = mz
index = utils.closest(mz, self.xvals)
self.gPeaks[id][1] = self.yvals[index]
def setSpeciesGivenMass(self, mass, xvals, yvals, peakFwhm, zs):
"""Similar to Species.setSpecies(). Except that instead of using
gPeaks, the Species() object is setup automatically when given
values for mass and the charges to be analysed.
"""
self.mass = mass
self.charges = zs
pseudogPeaks = {}
for z in zs:
xval = utils.get_mz(self.mass, z)
i = utils.closest(xval, xvals)
yval = yvals[i]
pseudogPeaks[z] = [xval, yval]
self.setSpecies(pseudogPeaks, peakFwhm)
def setSpeciesGivenMass(self,mass,xvals,yvals,peakFwhm,zs):
"""Similar to Species.setSpecies(). Except that instead of using
gPeaks, the Species() object is setup automatically when given
values for mass and the charges to be analysed.
"""
self.mass = mass
self.charges = zs
pseudogPeaks = {}
for z in zs:
xval = utils.get_mz(self.mass, z)
i = utils.closest(xval, xvals)
yval = yvals[i]
pseudogPeaks[z] = [xval,yval]
self.setSpecies(pseudogPeaks, peakFwhm)
def on_pick(self, event):
"""Check if peak picking is active. If it is draw vertical line at the
peak's m/z value and label with peak ID.
"""
if self.pickingActive:
if self.pickedAlready:
line = self.axMs.lines.pop(len(self.axMs.lines) - 1)
self.tempAnnotation.set_visible(False)
self.pickedValue = event.mouseevent.xdata
yval = self.ms.yvals[utils.closest(self.pickedValue,
self.ms.xvals)]
peakId = self.pickedPeakIdLimit #value controlled by gui
self.axMs.axvline(self.pickedValue, color='k')
self.tempAnnotation = self.axMs.annotate(str(peakId),
[self.pickedValue, yval])
self.draw()
self.pickedAlready = True