saveName=None, yMax=yMax, figSize=figSize, median=median, legendLoc='upper left', legendCols=2, normProtein='BSubL24')
num = ['AMP_L', 'AMP_U']
den = ['AMP_U', 'AMP_L', 'AMP_S']
filtPlots_45SPulse = plotDataSets(files45SPulse, names45SPulse, num, den, AllSubunits, '45S pulse', '[U+L]/[U+L+S]', reds,
saveName=None, yMax=yMax, figSize=figSize, median=median, legendLoc='upper left', legendCols=2, normProtein='BSubL01')
filtPlots_50SIF2Pulse = plotDataSets(files50SIF2Pulse, names50SIF2Pulse, num, den, AllSubunits, '50S IF2 pulse', '[U+L/[U+L+S]', blues,
saveName=None, yMax=yMax, figSize=figSize, median=median, legendLoc='upper left', legendCols=2, normProtein='BSubL01')
##################Merge data###########################
num = ['AMP_U']
den = ['AMP_U', 'AMP_S']
normProtein='BSubL24'
merged45 = qMS.mergeFiles(files45S, num, den, normProtein)
merged50 = qMS.mergeFiles(files50SIF2, num, den, normProtein)
verifiedZero = ['BSubL16', 'BSubL28', 'BSubL36', 'BSubL31a']
for i in verifiedZero:
merged45[i] = numpy.array([0.0])
##################Plot protein inventory data###########################
myPlot = vizLib.plotStatsDict(merged45, name='45SMerged', proteins=LargeSubunit, offset=0.4, markerSize=12, color='#e31a1c', yMax = 1.5, median=False)
myPlot = vizLib.addStatsDictToPlot(merged50, myPlot, name='50SMerged', offset=0.6, markerSize=12, color='#377db8', median=False)
myPlot.set_ylabel('protein occupancy\nnormalized to L24', multialignment='center')
myPlot.set_title('protein occupancy 45S vs. 50S')
pylab.legend(loc='lower left', prop={'size':12})
pylab.tight_layout()
pylab.show('all')
proteinToNormalizeTo = "BSubL24"
LargeSubunit = ['BSubL01', 'BSubL02', 'BSubL03', 'BSubL04', 'BSubL05', 'BSubL06', 'BSubL10', 'BSubL11',
'BSubL12', 'BSubL13', 'BSubL14', 'BSubL15', 'BSubL16', 'BSubL17', 'BSubL18', 'BSubL19', 'BSubL20', 'BSubL21',
'BSubL22', 'BSubL23', 'BSubL24', 'BSubL27', 'BSubL28', 'BSubL29', 'BSubL30', 'BSubL32',
'BSubL33a', 'BSubL35', 'BSubL36']
McMaster45S = [path+i for i in ["McMaster45S_esi-run1_filt.csv", "McMaster45S_esi-run2.1_filt.csv", "McMaster45S_esi-run2_filt.csv", "McMaster45S_qtof_filt_filtppm.csv"]]
McMaster50S = [path+i for i in ["McMaster50S_esi-run1_filt.csv", "McMaster50S_esi-run2.1_filt.csv", "McMaster50S_esi-run2_filt.csv", "McMaster50S_qtof_filt_filtppm.csv"]]
fileLists = [McMaster45S, McMaster50S]
merged = []
for listOfFiles in fileLists:
merged.append(qMS.mergeFiles(listOfFiles, pulse, numerator, denominator, proteinToNormalizeTo, LargeSubunit))
myPlot = qMS.makePlotWithDataSets(merged, LargeSubunit, ["McMaster45S_merged", 'McMaster50S_merged'])
for i in LargeSubunit:
pVal = stats.ttest_ind(merged[0][i]['vals'], merged[1][i]['vals'], equal_var=False)
print merged[0]['BSubL02']['vals']
print merged[1]['BSubL20']['vals']
L30ttest = stats.ttest_ind(merged[0]['BSubL02']['vals'], merged[1]['BSubL02']['vals'])
L12ttest = stats.ttest_ind(merged[0]['BSubL34']['vals'], merged[1]['BSubL34']['vals'])
print L30ttest
print L12ttest
##################Plot pool data vs. protein inventory data###########################
'''
verifiedZero = ['BSubL16', 'BSubL28', 'BSubL36']
for z in verifiedZero:
