def GeneratePlot(request):
"""
Input options from the analysis filtering html form is processed here and custom django database filtering procedures are automatically
specified. Labels for the plot are dynamically created based on the parameters included when the plotting method. The column name in the
relevant database table is specified through a django parameter to access the data relevant to this genetic analysis module.
"""
form = PlotCustomizationOptions(request.POST or None)
if request.method == 'POST':
if form.is_valid():
FilterThreshold = form.cleaned_data.get('FilterThreshold', 0)
if (form.cleaned_data.get('ArithmaticOperator',
0) == 'GreaterThan'):
return GeneticAnalysisTools.GeneratePlot.PlotData(
request,
GeneticDataRecords=ChiSquareAssociation.objects.all(
).filter(BonfCorrectedPValue__gt=FilterThreshold),
GeneticAttributeName='BonfCorrectedPValue',
PlotXLabel='SNP P-Value',
PlotYLabel='Number of SNPs',
PlotTitle='Total distribution of SNP P-Values')
elif (form.cleaned_data.get('ArithmaticOperator',
0) == 'GreaterThanOrEqual'):
return GeneticAnalysisTools.GeneratePlot.PlotData(
request,
GeneticDataRecords=ChiSquareAssociation.objects.all(
).filter(BonfCorrectedPValue__gte=FilterThreshold),
GeneticAttributeName='BonfCorrectedPValue',
PlotXLabel='SNP P-Value',
PlotYLabel='Number of SNPs',
PlotTitle='Total distribution of SNP P-Values')
elif (form.cleaned_data.get('ArithmaticOperator',
0) == 'LessThan'):
return GeneticAnalysisTools.GeneratePlot.PlotData(
request,
GeneticDataRecords=ChiSquareAssociation.objects.all(
).filter(BonfCorrectedPValue__lt=FilterThreshold),
GeneticAttributeName='BonfCorrectedPValue',
PlotXLabel='SNP P-Value',
PlotYLabel='Number of SNPs',
PlotTitle='Total distribution of SNP P-Values')
elif (form.cleaned_data.get('ArithmaticOperator',
0) == 'LessThanOrEqual'):
return GeneticAnalysisTools.GeneratePlot.PlotData(
request,
GeneticDataRecords=ChiSquareAssociation.objects.all(
).filter(BonfCorrectedPValue__lte=FilterThreshold),
GeneticAttributeName='BonfCorrectedPValue',
PlotXLabel='SNP P-Value',
PlotYLabel='Number of SNPs',
PlotTitle='Total distribution of SNP P-Values')
else:
return GeneticAnalysisTools.GeneratePlot.PlotData(
request,
GeneticDataRecords=ChiSquareAssociation.objects.all().filter(
BonfCorrectedPValue__gt=FilterThreshold),
GeneticAttributeName='BonfCorrectedPValue',
PlotXLabel='SNP P-Value',
PlotYLabel='Number of SNPs',
PlotTitle='Total distribution of SNP P-Values')
def ResultsTable(request):
form = PlotCustomizationOptions(request.POST or None)
if request.method == 'POST':
if form.is_valid():
FilterThreshold = form.cleaned_data.get('FilterThreshold', 0)
if (form.cleaned_data.get('ArithmaticOperator', 0)=='GreaterThan'):
return GeneticAnalysisTools.GenerateResultsTable.GenerateResultsTable(request, TableTitle='____________________Top SNPs____________________', TableColumnSummaryDescriptions=('Chromosome', 'SNP ID', 'Bonferroni Corrected P-Value'), TableColumnData=ChiSquareAssociation.objects.all().filter(BonfCorrectedPValue__gt=FilterThreshold).order_by('BonfCorrectedPValue')[:40], TableColumnNames=('Chromosome', 'SNP', 'BonfCorrectedPValue'))
elif (form.cleaned_data.get('ArithmaticOperator', 0)=='GreaterThanOrEqual'):
return GeneticAnalysisTools.GenerateResultsTable.GenerateResultsTable(request, TableTitle='____________________Top SNPs____________________', TableColumnSummaryDescriptions=('Chromosome', 'SNP ID', 'Bonferroni Corrected P-Value'), TableColumnData=ChiSquareAssociation.objects.all().filter(BonfCorrectedPValue__gte=FilterThreshold).order_by('BonfCorrectedPValue')[:40], TableColumnNames=('Chromosome', 'SNP', 'BonfCorrectedPValue'))
elif (form.cleaned_data.get('ArithmaticOperator', 0)=='LessThan'):
return GeneticAnalysisTools.GenerateResultsTable.GenerateResultsTable(request, TableTitle='____________________Top SNPs____________________', TableColumnSummaryDescriptions=('Chromosome', 'SNP ID', 'Bonferroni Corrected P-Value'), TableColumnData=ChiSquareAssociation.objects.all().filter(BonfCorrectedPValue__lt=FilterThreshold).order_by('BonfCorrectedPValue')[:40], TableColumnNames=('Chromosome', 'SNP', 'BonfCorrectedPValue'))
elif (form.cleaned_data.get('ArithmaticOperator', 0)=='LessThanOrEqual'):
return GeneticAnalysisTools.GenerateResultsTable.GenerateResultsTable(request, TableTitle='____________________Top SNPs____________________', TableColumnSummaryDescriptions=('Chromosome', 'SNP ID', 'Bonferroni Corrected P-Value'), TableColumnData=ChiSquareAssociation.objects.all().filter(BonfCorrectedPValue__lte=FilterThreshold).order_by('BonfCorrectedPValue')[:40], TableColumnNames=('Chromosome', 'SNP', 'BonfCorrectedPValue'))
else: return GeneticAnalysisTools.GenerateResultsTable.GenerateResultsTable(request, TableTitle='____________________Top SNPs____________________', TableColumnSummaryDescriptions=('Chromosome', 'SNP ID', 'Bonferroni Corrected P-Value'), TableColumnData=ChiSquareAssociation.objects.all().order_by('BonfCorrectedPValue')[:40], TableColumnNames=('Chromosome', 'SNP', 'BonfCorrectedPValue'))
def GeneratePlot(request):
"""
Input options from the analysis filtering html form is processed here and custom django database filtering procedures are automatically
specified. Labels for the plot are dynamically created based on the parameters included when the plotting method. The column name in the
relevant database table is specified through a django parameter to access the data relevant to this genetic analysis module.
"""
form = PlotCustomizationOptions(request.POST or None)
if request.method == 'POST':
if form.is_valid():
FilterThreshold = form.cleaned_data.get('FilterThreshold', 0)
if (form.cleaned_data.get('ArithmaticOperator', 0)=='GreaterThan'):
return GeneticAnalysisTools.GeneratePlot.PlotData(request,
GeneticDataRecords=ChiSquareAssociation.objects.all().filter(BonfCorrectedPValue__gt=FilterThreshold), GeneticAttributeName='BonfCorrectedPValue', PlotXLabel='SNP P-Value', PlotYLabel='Number of SNPs', PlotTitle='Total distribution of SNP P-Values')
elif (form.cleaned_data.get('ArithmaticOperator', 0)=='GreaterThanOrEqual'):
return GeneticAnalysisTools.GeneratePlot.PlotData(request,
GeneticDataRecords=ChiSquareAssociation.objects.all().filter(BonfCorrectedPValue__gte=FilterThreshold), GeneticAttributeName='BonfCorrectedPValue', PlotXLabel='SNP P-Value', PlotYLabel='Number of SNPs', PlotTitle='Total distribution of SNP P-Values')
elif (form.cleaned_data.get('ArithmaticOperator', 0)=='LessThan'):
return GeneticAnalysisTools.GeneratePlot.PlotData(request,
GeneticDataRecords=ChiSquareAssociation.objects.all().filter(BonfCorrectedPValue__lt=FilterThreshold), GeneticAttributeName='BonfCorrectedPValue', PlotXLabel='SNP P-Value', PlotYLabel='Number of SNPs', PlotTitle='Total distribution of SNP P-Values')
elif (form.cleaned_data.get('ArithmaticOperator', 0)=='LessThanOrEqual'):
return GeneticAnalysisTools.GeneratePlot.PlotData(request,
GeneticDataRecords=ChiSquareAssociation.objects.all().filter(BonfCorrectedPValue__lte=FilterThreshold), GeneticAttributeName='BonfCorrectedPValue', PlotXLabel='SNP P-Value', PlotYLabel='Number of SNPs', PlotTitle='Total distribution of SNP P-Values')
else: return GeneticAnalysisTools.GeneratePlot.PlotData(request, GeneticDataRecords=ChiSquareAssociation.objects.all().filter(BonfCorrectedPValue__gt=FilterThreshold), GeneticAttributeName='BonfCorrectedPValue', PlotXLabel='SNP P-Value', PlotYLabel='Number of SNPs', PlotTitle='Total distribution of SNP P-Values')
def ResultsTable(request):
form = PlotCustomizationOptions(request.POST or None)
if request.method == 'POST':
if form.is_valid():
FilterThreshold = form.cleaned_data.get('FilterThreshold', 0)
if (form.cleaned_data.get('ArithmaticOperator',
0) == 'GreaterThan'):
return GeneticAnalysisTools.GenerateResultsTable.GenerateResultsTable(
request,
TableTitle=
'____________________Top SNPs____________________',
TableColumnSummaryDescriptions=(
'Chromosome', 'SNP ID',
'Bonferroni Corrected P-Value'),
TableColumnData=ChiSquareAssociation.objects.all().filter(
BonfCorrectedPValue__gt=FilterThreshold).order_by(
'BonfCorrectedPValue')[:40],
TableColumnNames=('Chromosome', 'SNP',
'BonfCorrectedPValue'))
elif (form.cleaned_data.get('ArithmaticOperator',
0) == 'GreaterThanOrEqual'):
return GeneticAnalysisTools.GenerateResultsTable.GenerateResultsTable(
request,
TableTitle=
'____________________Top SNPs____________________',
TableColumnSummaryDescriptions=(
'Chromosome', 'SNP ID',
'Bonferroni Corrected P-Value'),
TableColumnData=ChiSquareAssociation.objects.all().filter(
BonfCorrectedPValue__gte=FilterThreshold).order_by(
'BonfCorrectedPValue')[:40],
TableColumnNames=('Chromosome', 'SNP',
'BonfCorrectedPValue'))
elif (form.cleaned_data.get('ArithmaticOperator',
0) == 'LessThan'):
return GeneticAnalysisTools.GenerateResultsTable.GenerateResultsTable(
request,
TableTitle=
'____________________Top SNPs____________________',
TableColumnSummaryDescriptions=(
'Chromosome', 'SNP ID',
'Bonferroni Corrected P-Value'),
TableColumnData=ChiSquareAssociation.objects.all().filter(
BonfCorrectedPValue__lt=FilterThreshold).order_by(
'BonfCorrectedPValue')[:40],
TableColumnNames=('Chromosome', 'SNP',
'BonfCorrectedPValue'))
elif (form.cleaned_data.get('ArithmaticOperator',
0) == 'LessThanOrEqual'):
return GeneticAnalysisTools.GenerateResultsTable.GenerateResultsTable(
request,
TableTitle=
'____________________Top SNPs____________________',
TableColumnSummaryDescriptions=(
'Chromosome', 'SNP ID',
'Bonferroni Corrected P-Value'),
TableColumnData=ChiSquareAssociation.objects.all().filter(
BonfCorrectedPValue__lte=FilterThreshold).order_by(
'BonfCorrectedPValue')[:40],
TableColumnNames=('Chromosome', 'SNP',
'BonfCorrectedPValue'))
else:
return GeneticAnalysisTools.GenerateResultsTable.GenerateResultsTable(
request,
TableTitle='____________________Top SNPs____________________',
TableColumnSummaryDescriptions=('Chromosome', 'SNP ID',
'Bonferroni Corrected P-Value'),
TableColumnData=ChiSquareAssociation.objects.all().order_by(
'BonfCorrectedPValue')[:40],
TableColumnNames=('Chromosome', 'SNP', 'BonfCorrectedPValue'))
