def calc_figureRightProtein(self):
self.PLPlotProtein.clear()
self.proteinView = self.dataFrame[self.dataFrame[PROTEINHEADER] == self.currentRow[PROTEINHEADER]]
self.passProteinView = self.proteinView[self.proteinView['allClear'] == True]
self.failProteinView = self.proteinView[self.proteinView['allClear'] == False]
theRows = self.proteinView[self.proteinView['TID'] == self.currentRow['TID']]
self.selectedPairedPointsProtein, = self.PLPlotProtein.plot(theRows['currentPosProtein'], theRows['currentCalc'], 'o', ms=30*self.size, alpha=0.25, color='red')
self.selectedPointProtein, = self.PLPlotProtein.plot(self.currentRow['currentPosProtein'], self.currentRow['currentCalc'],
'o', ms=20, alpha=0.5, color='yellow', visible=True)
self.PLPlotProtein.plot(self.passProteinView['currentPosProtein'], self.passProteinView['currentCalc'], 'ro', picker=5, label="Saved : " + str(len(self.passProteinView['currentCalc'].values)))
meds = self.determineMedians(self.passProteinView, 'currentPosProtein')
self.PLPlotProtein.plot(meds[0], meds[1], 'g-', lw=2, label="Median : " + str(round(numpy.median(meds[1]),1)))
if not self.hideCheck.IsChecked():
self.PLPlotProtein.plot(self.failProteinView['currentPosProtein'], self.failProteinView['currentCalc'], 'x', mec='grey', picker=5, label="Filtered : " + str(len(self.failProteinView['currentCalc'].values)))
self.PLPlotProtein.grid(self.cb_grid.IsChecked())
self.PLPlotProtein.set_xticks(range(1,int(self.dataFrame['currentPosProtein'].max())+1))
self.PLPlotProtein.set_xticklabels(self.positionLabelsProtein, rotation=30, size='small')
self.PLPlotProtein.set_title(self.currentRow[PROTEINHEADER] + " : " + setCurrentFrac(self.calcNum, self.calcDen))
self.PLPlotProtein.set_xlim([0,self.dataFrame['currentPosProtein'].max()+1])
if not self.zoomCheck.IsChecked():
self.PLPlotProtein.set_ylim([0,max(self.passProteinView['currentCalc'].max(),1)])
else:
self.PLPlotProtein.set_ylim([0,3])
self.PLPlotProtein.legend()
vizLib.cleanAxis(self.PLPlotProtein, ticksOnly=True)
def calc_figureLeft(self):
self.PLPlotDataset.clear()
self.datasetView = self.dataFrame[self.dataFrame[FILENAMEHEADER] == self.currentRow[FILENAMEHEADER]]
self.passDatasetView = self.datasetView[self.datasetView['allClear'] == True]
self.failDatasetView = self.datasetView[self.datasetView['allClear'] == False]
self.selectedPointDataset, = self.PLPlotDataset.plot(self.currentRow['currentPosDataset'], self.currentRow['currentCalc'],
'o', ms=20, alpha=0.5, color='yellow', visible=True)
self.PLPlotDataset.grid(self.cb_grid.IsChecked())
self.PLPlotDataset.plot(self.passDatasetView['currentPosDataset'], self.passDatasetView['currentCalc'], 'ro', picker=5, label="Saved : " + str(len(self.passDatasetView['currentCalc'].values)))
meds = self.determineMedians(self.passDatasetView, 'currentPosDataset')
self.PLPlotDataset.plot(meds[0], meds[1], 'g-', lw=2, label="Median : " + str(round(numpy.median(meds[1]),1)))
if not self.hideCheck.IsChecked():
self.PLPlotDataset.plot(self.failDatasetView['currentPosDataset'], self.failDatasetView['currentCalc'], 'x', mec='grey', picker=5, label="Filtered : " + str(len(self.failDatasetView['currentCalc'].values)))
self.PLPlotDataset.set_xticks(range(1,int(self.dataFrame['currentPosDataset'].max())+1))
self.PLPlotDataset.set_xticklabels(self.positionLabelsDataset, rotation=90, size='small')
self.PLPlotDataset.set_title(self.currentRow[FILENAMEHEADER] + " : " + setCurrentFrac(self.calcNum, self.calcDen))
if self.proteinZoomOn.IsChecked():
(x_low, x_high) = map(float, self.proteinZoomRangeBypass.GetValue().split(' '))
self.PLPlotDataset.set_xlim([x_low,x_high])
else:
self.PLPlotDataset.set_xlim([0.5,self.datasetView['currentPosDataset'].max()+1.5])
if not self.zoomCheck.IsChecked():
self.PLPlotDataset.set_ylim([0,max(self.passDatasetView['currentCalc'].max(),1)])
else:
self.PLPlotDataset.set_ylim([0,3])
self.PLPlotDataset.legend()
vizLib.cleanAxis(self.PLPlotDataset, ticksOnly=True)
def calc_figureRightFit(self):
plotsfile = self.datapath+self.currentRow[ISOFILEHEADER]+'.plots'
txtfile = self.datapath+self.currentRow[ISOFILEHEADER]+'.txt'
df = pandas.read_csv(plotsfile)
df2 = pandas.read_csv(txtfile, header=None, sep=' ')
del df['residAdj']
self.PNGPlot.clear()
self.PNGPlot.plot(df2[0][0:len(df['dat'])].values, df['dat'].values, 'o', markersize=6, markerfacecolor='None', markeredgecolor='red')
self.PNGPlot.plot(df2[0][0:len(df['dat'])].values, df['dat'].values, 'r-', linewidth=2, label='data')
self.PNGPlot.plot(df2[0][0:len(df['fit'])].values, df['fit'].values, 'b-', linewidth=2, label='fit')
self.PNGPlot.plot(df2[0][0:len(df['resid'])].values, df['resid'].values, 'g-', linewidth=2, label='residual')
self.PNGPlot.set_xlim(df2[0][0:len(df['dat'])].values.min(), df2[0][0:len(df['dat'])].values.max())
self.PNGPlot.legend()
stringColor = 'black'
row = self.currentRow
if row['handDelete']:
stringColor = 'red'
elif row['handSave']:
stringColor = 'green'
seqText = str(self.currentRow['seqmod']) + " : z=" + str(self.currentRow['charge'])
dataString1 = "ppmDiff: " + str(round(row['ppmDiff'],1)) + " : " + str(row['ppmDiff_pass']) +\
"\nN14: " + str(round(row['ppm_n14'],1)) + " : " + str(row['ppm_n14_pass']) +\
"\nN15: " + str(round(row['ppm_n15'],1)) + " : " + str(row['ppm_n15_pass']) +\
"\nresid: " + str(round(row['resid'],1)) + " : " + str(row['resid_pass'])
dataString2 = "ratio: " + str(round(row['currentCalc'],1)) + " : " + str(row['ratio_pass']) +\
"\nintensity: " + str(round(row['minIntensity'],1)) + " : " + str(row['minInt_pass']) +\
"\n"+self.lastHistField+" "+ str(round(row[self.lastHistField],1)) + " : " + str(row[self.lastHistField+'_pass']) +\
"\ncurrentCalc: " + str(round(row['currentCalc'],1))
self.PNGPlot.text(0.02, 0.98,seqText,
horizontalalignment='left',
verticalalignment='top',
transform = self.PNGPlot.transAxes,
color = stringColor,
size='large')
self.PNGPlot.text(0.98, 0.02,dataString1,
horizontalalignment='right',
verticalalignment='bottom',
transform = self.PNGPlot.transAxes,
color = stringColor)
self.PNGPlot.text(0.02, 0.02,dataString2,
horizontalalignment='left',
verticalalignment='bottom',
transform = self.PNGPlot.transAxes,
color = stringColor)
self.PNGPlot.set_title(self.currentRow[UIDHEADER])
self.PNGPlot.yaxis.set_major_formatter(matplotlib.ticker.FormatStrFormatter('%.0e'))
vizLib.cleanAxis(self.PNGPlot, ticksOnly=True)
def calc_hists(self):
hists = {'ppmDiff':self.hist1, 'ppm_n14':self.hist2, 'ppm_n15':self.hist3, 'resid':self.hist4, 'minIntensity':self.hist5, self.lastHistField:self.hist6}
relSet = self.dataFrame[(self.dataFrame[FILENAMEHEADER] == self.currentRow[FILENAMEHEADER]) & (self.dataFrame['allClear'] == True)]
for curHist in hists.keys():
hists[curHist].clear()
data = relSet[curHist].values
bin_num = min(20, len(list(set(data))))
if curHist == 'minIntensity' or curHist == 'resid':
bin_num = numpy.logspace(numpy.log10(data.min()), numpy.log10(data.max()), num=20)
hists[curHist].hist(data, bins = bin_num)
hists[curHist].text(0.05,0.75,curHist, transform=hists[curHist].transAxes)
numTicks = 2
spacing = (data.max()-data.min())/(numTicks+2)
if curHist == 'minIntensity' or curHist == 'resid':
hists[curHist].set_xscale('log')
else:
hists[curHist].set_xticks([data.min()+spacing*i for i in range(numTicks+3)])
hists[curHist].set_xticklabels([str(round(data.min()+spacing*i,1)) for i in range(numTicks+3)], size='small')
hists[curHist].set_xlim(data.min(), data.max())
hists[curHist].set_yticks([])
vizLib.cleanAxis(hists[curHist])
def prettyPlot3TransMRM(dataFrame, toPlotIndex, figsize=(33, 8.5)):
axisArray = []
pylab.figure(figsize=figsize)
for i in range(len(toPlotIndex)):
a = plt.subplot2grid((2, 9), (0, i * 3), colspan=1, rowspan=2)
a = plotTotalChromPairsMRM(dataFrame, toPlotIndex[i], a, smooth=5, zoom=True)
info = getInfoMRM(dataFrame, toPlotIndex[i])
a.set_title(info[1])
vizLib.tickNum(a, xAxis=4, yAxis=4)
vizLib.cleanAxis(a, ticksOnly=True)
axisArray.append(a)
b = plt.subplot2grid((2, 9), (0, i * 3 + 1), colspan=2, rowspan=1)
b = plotAllTransitionsMRM(dataFrame, toPlotIndex[i], b, smooth=5, zoom=True)
info = getInfoMRM(dataFrame, toPlotIndex[i])
b.set_title("light")
vizLib.tickNum(b, xAxis=4, yAxis=4)
vizLib.cleanAxis(b, ticksOnly=True)
axisArray.append(b)
c = plt.subplot2grid((2, 9), (1, i * 3 + 1), colspan=2, rowspan=1)
opp = getPairedIonMRM(dataFrame, toPlotIndex[i])
c = plotAllTransitionsMRM(dataFrame, opp, c, smooth=5, zoom=True)
info = getInfoMRM(dataFrame, toPlotIndex[i])
c.set_title("heavy")
vizLib.tickNum(c, xAxis=4, yAxis=4)
vizLib.cleanAxis(c, ticksOnly=True)
axisArray.append(c)
pylab.tight_layout()
return axisArray