def intersections_table(request,
ratio=2.,
pvalue=0.05,
fold_change=None,
exp=None,
set=None,
benjamini=None):
id = 'seq_id'
ratio = float(ratio)
pvalue = float(pvalue)
if fold_change == "None": fold_change = None
if exp == "None": exp = None
if benjamini == "None": benjamini = None
filter = TranscriptFilterSet(request.GET, transcripts)
intersections = []
#signatures = Signature.objects.differential(ratio, pvalue) #
if set:
set = Set.objects.get(pk=set)
signatures = set.signatures.all()
else:
set = Set.objects.get(pk=1)
signatures = set.signatures.all()
for signature in signatures: #
signature.differential(
ratio, pvalue, fold_change, exp, benjamini,
id) # Might a good function for a custom manager.
# Construct table:
rows = []
row = ['Signature']
limit = len(signatures)
for a_signature in signatures:
row.append(a_signature.name)
row_count = 0
rows.append("\t".join(row))
for row_number, a_signature in enumerate(signatures):
row = [a_signature.name]
for column_number, another_signature in enumerate(signatures):
if column_number == row_number:
intersection = ''
elif column_number <= row_number:
intersection = Intersection(a_signature, another_signature)
intersection = "%s" % (pf(intersection.up_pvalue, 1)) #/%s
#pf(intersection.diff_pvalue, 1),
#)#pf(intersection.down_pvalue, 1)
else:
intersection = Intersection(a_signature, another_signature)
intersection = "%s" % (
len(intersection.up)
) #) #/%s/%slen(intersection.diff),, len(intersection.down
row.append(intersection)
rows.append("\t".join(row))
table = "Table: Intersections\n~~~~~~~~~~~~~~~~~~~~~~\n" + "\n".join(rows)
ctx = {'title': 'Intersections', 'table': table}
return render(request, 'expressions/intersections_table.html', ctx)
def meta(request,
ratio=2.,
pvalue=0.05,
fold_change=None,
exp=None,
set=None,
benjamini=None):
"""Common to all signature in a category."""
terms = False
id = 'seq_id'
if request.GET:
if 'ratio' in request.GET and request.GET['ratio']:
ratio = float(request.GET['ratio'])
if 'pvalue' in request.GET and request.GET['pvalue']:
pvalue = float(request.GET['pvalue'])
if 'benjamini' in request.GET and request.GET['benjamini']:
benjamini = float(request.GET['benjamini'])
if 'fold_change' in request.GET and request.GET['fold_change']:
fold_change = float(request.GET['fold_change'])
if 'expression__exp' in request.GET and request.GET['expression__exp']:
exp = float(request.GET['expression__exp'])
if 'set' in request.GET and request.GET['set']:
set = request.GET['set']
if 'terms' in request.GET and request.GET['terms']:
terms = True
if 'id' in request.GET['id'] and request.GET['id']:
id = request.GET['id']
entry = get("Meta-Analysis")
set = Set.objects.get(pk=set or 1)
signatures = set.signatures.all()
for signature in signatures:
signature.differential(ratio, pvalue, fold_change, exp, benjamini, id)
signatures = Signatures(signatures)
filter = TranscriptFilterSet(request.GET, transcripts)
if terms:
table_up = functional_enrichment(terms, signatures.up, id)
table_down = functional_enrichment(terms, signatures.down, id)
#table_diff = functional_enrichment(terms, list(chain(signatures.up, signatures.down, id)))
table_diff = None
else:
table_up = table_down = table_diff = None
ctx = {
'title': 'Meta-Analysis',
'entry': entry,
'signatures': signatures,
'filter': filter,
'sets': Set.objects.all(),
'terms': terms,
'table_up': table_up,
'table_down': table_down,
'table_diff': table_diff,
'ids': IDs,
'id': id,
}
return render_to_response('expressions/meta.html',
ctx,
context_instance=RequestContext(request))
def transcript_list(request):
f = TranscriptFilterSet(request.GET, queryset=Transcript.objects.all())
return render_to_response('expressions/transcripts.html', {'filter': f},
context_instance=RequestContext(request))
def transcripts(request):
filterset = TranscriptFilterSet(request.GET or None)
return render_to_response('expressions/transcripts.html',
{'filterset': filterset},
context_instance=RequestContext(request))
def intersection(request,
a,
another,
ratio=2.,
pvalue=0.05,
fold_change=None,
exp=None,
benjamini=None):
terms = None
id = 'seq_id'
a_signature = Signature.objects.get(pk=a)
another_signature = Signature.objects.get(pk=another)
if request.GET:
if 'ratio' in request.GET and request.GET['ratio']:
ratio = request.GET['ratio']
if 'pvalue' in request.GET and request.GET['pvalue']:
pvalue = request.GET['pvalue']
if 'benjamini' in request.GET and request.GET['benjamini']:
benjamini = request.GET['benjamini']
if 'fold_change' in request.GET and request.GET['fold_change']:
fold_change = request.GET['fold_change']
print "get fold_change", fold_change
if 'expression__exp' in request.GET and request.GET['expression__exp']:
exp = float(request.GET['expression__exp'])
if 'id' in request.GET and request.GET['id']:
id = request.GET['id']
if 'terms' in request.GET and request.GET['terms']:
terms = True
else:
terms = False
filter = TranscriptFilterSet(request.GET, transcripts)
if fold_change == 'None':
fold_change = None
#print fold_change
a_signature.differential(float(ratio), float(pvalue),
float(fold_change or 0), exp, benjamini, id)
another_signature.differential(float(ratio), float(pvalue),
float(fold_change or 0), exp, benjamini, id)
intersection = Intersection(a_signature, another_signature)
table_up = functional_enrichment(terms, intersection.upregulated(), id)
table_down = functional_enrichment(terms, intersection.downregulated(), id)
ctx = {
'title': '%s & %s' % (a_signature, another_signature),
'intersection': intersection,
'a_signature': a_signature,
'another_signature': another_signature,
'filer': filter,
'terms': terms,
'table_up': table_up,
'table_down': table_down,
'ids': IDs,
'id': id,
}
return render_to_response('expressions/intersection.html/',
ctx,
context_instance=RequestContext(request))
def intersections(request,
ratio=2.,
pvalue=0.05,
fold_change=None,
exp=None,
set=None,
benjamini=None):
entry = get("Intersections")
id = 'seq_id'
if request.GET:
if 'ratio' in request.GET and request.GET['ratio']:
ratio = float(request.GET['ratio'])
if 'pvalue' in request.GET and request.GET['pvalue']:
pvalue = float(request.GET['pvalue'])
if 'fold_change' in request.GET and request.GET['fold_change']:
fold_change = float(request.GET['fold_change'])
if 'benjamini' in request.GET and request.GET['benjamini']:
benjamini = float(request.GET['benjamini'])
if 'expression__exp' in request.GET and request.GET['expression__exp']:
exp = request.GET['expression__exp']
print "Expression exp"
if 'set' in request.GET and request.GET['set']:
set = request.GET['set']
if 'id' in request.GET and request.GET['id']:
id = request.GET['id']
filter = TranscriptFilterSet(request.GET, transcripts)
intersections = []
#signatures = Signature.objects.differential(ratio, pvalue) #
if set:
set = Set.objects.get(pk=set)
signatures = set.signatures.all()
else:
set = Set.objects.get(pk=1)
signatures = set.signatures.all()
for signature in signatures: #
signature.differential(
ratio, pvalue, fold_change, exp, benjamini,
id) # Might a good function for a custom manager.
for a_signature in signatures:
for another_signature in signatures[:len(
signatures
)]: # Prevents duplicated comparisions the other way around.
if a_signature != another_signature: # Prevent comparision of the same signatures and
intersection = Intersection(a_signature, another_signature)
#print intersection.name, len(intersection.up), len(intersection.down)
intersections.append(intersection)
# Context:
ctx = {
'title': 'Intersections',
'entry': entry,
'signatures': signatures,
'intersections': intersections,
'ratio': ratio,
'pvalue': pvalue,
'benjamini': benjamini,
'fold_change': fold_change,
'exp': exp,
'filter': filter,
'sets': Set.objects.all(),
'ids': IDs,
'id': id,
'set': set,
}
return render_to_response('expressions/intersections.html',
ctx,
context_instance=RequestContext(request))
def signature(request,
pk=None,
ratio=2.,
pvalue=0.05,
fold_change=None,
exp=None,
benjamini=None,
name=None):
terms = False
id = 'seq_id'
term = "factors"
if request.GET:
if 'ratio' in request.GET and request.GET['ratio']:
ratio = float(request.GET['ratio'])
if 'pvalue' in request.GET and request.GET['pvalue']:
pvalue = float(request.GET['pvalue'])
if 'benjamini' in request.GET and request.GET['benjamini']:
benjamini = float(request.GET and request.GET['benjamini'])
if 'expression__exp' in request.GET and request.GET['expression__exp']:
exp = float(request.GET['expression__exp'])
if 'id' in request.GET and request.GET['id']:
id = request.GET['id']
if 'terms' in request.GET and request.GET['terms']:
terms = True
else:
terms = False
if 'term' in request.GET and request.GET['term']:
term = request.GET['term']
else:
term = "factors"
elif 'term' in request.POST:
term = request.POST['term']
print(term)
if pk: signature = Signature.objects.get(pk=pk)
elif name: signature = Signature.objects.get(name=name)
if not exp:
transcripts = signature.transcripts.filter((Q(ratio__gt=ratio)
| Q(ratio__lt=1. / ratio))
& Q(pvalue__lt=pvalue))
else: # What is about a gene that is only low expressed in one condition?
#print "Filtering on expression:"
transcripts = signature.transcripts.filter(
(Q(ratio__gt=ratio)
| Q(ratio__lt=1. / ratio))
& Q(pvalue__lt=pvalue
#& Q(expression__exp__gt=exp) & Q(expression__ctr__gt=exp)
))
transcripts = transcripts.filter(expression__exp__gt=exp,
expression__ctr__gt=exp)
if request.GET:
if 'symbol' in request.GET and request.GET['symbol']:
symbol = request.GET['symbol']
transcripts = transcripts.filter(symbol__icontains=symbol)
if 'fold_change' in request.GET and request.GET['fold_change']:
fold_change = float(request.GET['fold_change'])
#print len(transcripts)
transcripts = transcripts.filter(
Q(fold_change__gt=fold_change)
| Q(fold_change__lt=1. / fold_change))
#print "filtered transcripts", len(transcripts)
if 'benjamini' in request.GET and request.GET['benjamini']:
benjamini = float(request.GET['benjamini'])
transcripts = transcripts.filter(benjamini__lt=benjamini)
filter = TranscriptFilterSet(request.GET, transcripts)
#print type(filter), vars(filter)
#print len(filter.queryset)
table = TranscriptTable(filter.queryset)
RequestConfig(request).configure(table)
transcripts_up = transcripts.filter(
Q(ratio__gt=ratio)
& Q(pvalue__lt=pvalue))
transcripts_down = transcripts.filter(
Q(ratio__lt=1. / ratio)
& Q(pvalue__lt=pvalue))
table_up = functional_enrichment(terms, transcripts_up)
table_down = functional_enrichment(terms, transcripts_down)
#table_diff = functional_enrichment(terms, list(chain(transcripts_up, transcripts_down)))
table_diff = None
#print id
transcripts_up = set(
[getattr(transcript, id) for transcript in transcripts_up])
if None in transcripts_up: transcripts_up.remove(None)
transcripts_down = set(
[getattr(transcript, id) for transcript in transcripts_down])
if None in transcripts_down: transcripts_down.remove(None)
#transcripts_diff = set([getattr(transcripts, id) for transcript in transcripts_diff])
#if None in transcripts_diff: transcripts_diff.remove(None)
ctx = {
'signature': signature,
'transcripts': transcripts,
'transcripts_up': transcripts_up,
'transcripts_down': transcripts_down,
#'transcripts_diff': transcripts_diff,
'table': table,
'ratio': ratio,
'pvalue': pvalue,
'benjamini': benjamini,
'filter': filter,
'terms': terms,
'table_up': table_up,
'table_down': table_down,
'table_diff': table_diff,
'ids': IDs,
'id': id,
'term': term # GO term for go_filter
}
return render_to_response('expressions/signature.html',
ctx,
context_instance=RequestContext(request))