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)
