def testPlots2HLA3DPlotly(self): """ Make a 3D plot of BLAST bit scores, Z scores, and light matter scores. """ for parameterSet in testArgs.parameterSets: affinity = _AFFINITY[parameterSet] dirName = makeOutputDir(DATASET, parameterSet, '3d-plotly') for subject in SUBJECTS: zScores = [] bitScores = [] lmScores = [] labels = [] for query in QUERIES: if query.id != subject.id: bitScores.append(BIT_SCORES[query.id][subject.id]) zScores.append(Z_SCORES[query.id][subject.id]) lmScore = getScore(affinity, query.id, subject.id) lmScores.append(lmScore) labels.append(pythonNameToPdbName(query.id)) plot3DPlotly(bitScores, zScores, lmScores, subject.id, dirName, interactive=testArgs.interactive, labels=labels)
def testNonMatchingPlots2HLAAgainstPolymerase(self): """ Examine the correlation between light matter scores and BLAST bit scores. """ scoreTypeX = 'Light matter score' scoreTypeY = 'Bit score' for parameterSet in testArgs.parameterSets: affinity = _AFFINITY[parameterSet] dirName = makeOutputDir( DATASET, parameterSet, '%s-%s' % (FILESYSTEM_NAME[scoreTypeX], FILESYSTEM_NAME[scoreTypeY])) for subject in SUBJECTS: lmScores = [] bitScores = [] for query in QUERIES: if query.id != subject.id: bitScores.append(BIT_SCORES[query.id][subject.id]) lmScore = getScore(affinity, query.id, subject.id) lmScores.append(lmScore) plot(lmScores, bitScores, subject.id, scoreTypeX, scoreTypeY, dirName)
def testPlotsHA(self): """ Examine the correlation between BLAST bit scores and Z scores. """ scoreTypeX = 'Bit score' scoreTypeY = 'Z score' for parameterSet in testArgs.parameterSets: dirName = makeOutputDir( DATASET, parameterSet, '%s-%s' % (FILESYSTEM_NAME[scoreTypeX], FILESYSTEM_NAME[scoreTypeY])) allZScores = [] allBitScores = [] for queryId in BIT_SCORES: zScores = [] bitScores = [] for subjectId in BIT_SCORES[queryId]: if queryId != subjectId: bitScores.append(BIT_SCORES[queryId][subjectId]) zScores.append(Z_SCORES[queryId][subjectId]) allZScores.extend(zScores) allBitScores.extend(bitScores) plot(bitScores, zScores, queryId, scoreTypeX, scoreTypeY, dirName) plot(allBitScores, allZScores, 'all', scoreTypeX, scoreTypeY, dirName)
def testPlotsHA(self): """ Examine the correlation between our scores and blast bit scores. """ scoreTypeX = 'Light matter score' scoreTypeY = 'Bit score' for parameterSet in testArgs.parameterSets: affinity = _AFFINITY[parameterSet] dirName = makeOutputDir( DATASET, parameterSet, '%s-%s' % (FILESYSTEM_NAME[scoreTypeX], FILESYSTEM_NAME[scoreTypeY])) allBitScores = [] allLmScores = [] for queryId in BIT_SCORES: bitScores = [] lmScores = [] for subjectId in BIT_SCORES[queryId]: if queryId != subjectId: lmScore = getScore(affinity, queryId, subjectId) lmScores.append(lmScore) bitScores.append(BIT_SCORES[queryId][subjectId]) allBitScores.extend(bitScores) allLmScores.extend(lmScores) plot(lmScores, bitScores, queryId, scoreTypeX, scoreTypeY, dirName) plot(allLmScores, allBitScores, 'all', scoreTypeX, scoreTypeY, dirName)
def test3DHA(self): """ Make a 3D plot of BLAST bit scores, Z scores, and light matter scores. """ for parameterSet in testArgs.parameterSets: affinity = _AFFINITY[parameterSet] dirName = makeOutputDir(DATASET, parameterSet, '3d') allZScores = [] allBitScores = [] allLmScores = [] for queryId in sorted(BIT_SCORES): zScores = [] bitScores = [] lmScores = [] for subjectId in BIT_SCORES[queryId]: if queryId != subjectId: bitScores.append(BIT_SCORES[queryId][subjectId]) zScores.append(Z_SCORES[queryId][subjectId]) lmScore = getScore(affinity, queryId, subjectId) lmScores.append(lmScore) allZScores.extend(zScores) allBitScores.extend(bitScores) allLmScores.extend(lmScores) plot3D(bitScores, zScores, lmScores, queryId, 'Bit score', 'Z score', 'Light matter score', dirName, testArgs.interactive) # Plot all scores on one plot. plot3D(allBitScores, allZScores, allLmScores, 'all', 'Bit score', 'Z score', 'Light matter score', dirName, testArgs.interactive)
def testPlotsHA3DPlotly(self): """ Make a 3D plot of BLAST bit scores, Z scores, and light matter scores. """ for parameterSet in testArgs.parameterSets: affinity = _AFFINITY[parameterSet] dirName = makeOutputDir(DATASET, parameterSet, '3d-plotly') allZScores = [] allBitScores = [] allLmScores = [] allLabels = [] for queryId in sorted(BIT_SCORES): zScores = [] bitScores = [] lmScores = [] labels = [] for subjectId in BIT_SCORES[queryId]: if queryId != subjectId: bitScores.append(BIT_SCORES[queryId][subjectId]) zScores.append(Z_SCORES[queryId][subjectId]) lmScore = getScore(affinity, queryId, subjectId) lmScores.append(lmScore) labels.append(pythonNameToPdbName(subjectId)) allLabels.append('%s vs. %s' % (pythonNameToPdbName(queryId), pythonNameToPdbName(subjectId))) allZScores.extend(zScores) allBitScores.extend(bitScores) allLmScores.extend(lmScores) plot3DPlotly(bitScores, zScores, lmScores, queryId, dirName, interactive=testArgs.interactive, labels=labels) if testArgs.interactive: response = input('Continue? ') if response and response[0].lower() == 'n': return # Plot all scores on one plot. plot3DPlotly(allBitScores, allZScores, allLmScores, 'all', dirName, interactive=testArgs.interactive, labels=allLabels) if testArgs.interactive: response = input('Continue? ') if response and response[0].lower() == 'n': return
def testPlots2HLA3D(self): """ Make a 3D plot of BLAST bit scores, Z scores, and light matter scores. """ for parameterSet in testArgs.parameterSets: affinity = _AFFINITY[parameterSet] dirName = makeOutputDir(DATASET, parameterSet, '3d') for subject in SUBJECTS: zScores = [] bitScores = [] lmScores = [] for query in QUERIES: if query.id != subject.id: bitScores.append(BIT_SCORES[query.id][subject.id]) zScores.append(Z_SCORES[query.id][subject.id]) lmScore = getScore(affinity, query.id, subject.id) lmScores.append(lmScore) plot3D(bitScores, zScores, lmScores, subject.id, 'Bit score', 'Z score', 'Light matter score', dirName, testArgs.interactive)
def testPlots2HLA(self): """ Examine the correlation between BLAST bit scores and Z scores. """ scoreTypeX = 'Bit score' scoreTypeY = 'Z score' for parameterSet in testArgs.parameterSets: dirName = makeOutputDir( DATASET, parameterSet, '%s-%s' % (FILESYSTEM_NAME[scoreTypeX], FILESYSTEM_NAME[scoreTypeY])) for subject in SUBJECTS: bitScores = [] zScores = [] for query in QUERIES: if query.id != subject.id: zScores.append(Z_SCORES[query.id][subject.id]) bitScores.append(BIT_SCORES[query.id][subject.id]) plot(bitScores, zScores, subject.id, scoreTypeX, scoreTypeY, dirName)
def testPlots4PH0(self): """ Examine the correlation between light matter scores and Z scores. """ scoreTypeX = 'Light matter score' scoreTypeY = 'Z score' for parameterSet in testArgs.parameterSets: affinity = _AFFINITY[parameterSet] dirName = makeOutputDir( DATASET, parameterSet, '%s-%s' % (FILESYSTEM_NAME[scoreTypeX], FILESYSTEM_NAME[scoreTypeY])) for subject in SUBJECTS: lmScores = [] zScores = [] for query in QUERIES: if query.id != subject.id: zScores.append(Z_SCORES[query.id][subject.id]) lmScore = getScore(affinity, query.id, subject.id) lmScores.append(lmScore) plot(lmScores, zScores, subject.id, scoreTypeX, scoreTypeY, dirName)