def __init__(self, a_signature, another_signature):
self.a = a_signature
self.another = another_signature
self.name = "%s <-> %s" % (a_signature.link, another_signature.link)
self.up = a_signature.up & another_signature.up
self.down = a_signature.down & another_signature.down
self.diff = (a_signature.up | a_signature.down) \
& (another_signature.up | another_signature.down)
self.diff_pvalue = hyperg(len(a_signature.diff),
len(another_signature.diff),
a_signature.transcripts.count(),
len(self.diff))
self.down_pvalue = hyperg(len(a_signature.down),
len(another_signature.down),
a_signature.transcripts.count(),
len(self.down))
self.up_pvalue = hyperg(len(a_signature.up), len(another_signature.up),
a_signature.transcripts.count(), len(self.up))
self.anti_a = a_signature.up & another_signature.down
self.anti_b = a_signature.down & another_signature.up
self.anti_a_pvalue = hyperg(len(a_signature.up),
len(another_signature.down),
a_signature.transcripts.count(),
len(self.anti_a))
self.anti_b_pvalue = hyperg(len(a_signature.down),
len(another_signature.up),
a_signature.transcripts.count(),
len(self.anti_b))
def __init__(self, a_signature, another_signature):
self.a = a_signature
self.another = another_signature
self.name = "%s <-> %s" % (a_signature.link, another_signature.link)
self.up = a_signature.up & another_signature.up
self.down = a_signature.down & another_signature.down
self.diff = (a_signature.up | a_signature.down) & (another_signature.up | another_signature.down)
self.diff_pvalue = hyperg(
len(a_signature.diff), len(another_signature.diff), a_signature.transcripts.count(), len(self.diff)
)
self.down_pvalue = hyperg(
len(a_signature.down), len(another_signature.down), a_signature.transcripts.count(), len(self.down)
)
self.up_pvalue = hyperg(
len(a_signature.up), len(another_signature.up), a_signature.transcripts.count(), len(self.up)
)
self.anti_a = a_signature.up & another_signature.down
self.anti_b = a_signature.down & another_signature.up
self.anti_a_pvalue = hyperg(
len(a_signature.up), len(another_signature.down), a_signature.transcripts.count(), len(self.anti_a)
)
self.anti_b_pvalue = hyperg(
len(a_signature.down), len(another_signature.up), a_signature.transcripts.count(), len(self.anti_b)
)
def compara(self, S1, S2):
"""Compares two signatures for significant overlap."""
if isinstance(S1, str):
S1 = self[S1] # if only the name is given
if isinstance(S2, str):
S2 = self[S2] # the signature will be identfied
if len(S1) > len(S2):
total = len(S1)
else:
total = len(S2)
S1_ranked_list = []
S2_ranked_list = []
for gene in S1:
S1_ranked_list.append((S1[gene].ratio, S1[gene]))
S1_ranked_list.sort()
# S1_ranked_list.reverse()
for gene in S2:
S2_ranked_list.append((S2[gene].ratio, S2[gene]))
S2_ranked_list.sort()
# S2_ranked_list.reverse()
print len(S1_ranked_list), len(S2_ranked_list)
for threshold in xrange(100, 5000, 100):
S1.up = {}
S2.up = {}
for ratio, s1 in S1_ranked_list[:threshold]:
S1.up[s1.id] = s1
for ratio, s2 in S2_ranked_list[:threshold]:
S2.up[s2.id] = s2
Intersection = set(S1.up) & set(S2.up)
pvalue = hyperg(len(S1.up), len(S2.up), total, len(Intersection))
print threshold, "\t", len(S1.up), "\t", len(S2.up), "\t", len(
Intersection
), "\t", pvalue # len(IntersectionUp), pvalueUp, len(S1.down), len(S2.down), len(IntersectionDown), pvalueDown, len(IntersectionComb), pvalueComb
def compara(self, S1, S2):
"""Compares two signatures for significant overlap."""
if isinstance(S1, str): S1 = self[S1] # if only the name is given
if isinstance(S2, str):
S2 = self[S2] # the signature will be identfied
if len(S1) > len(S2): total = len(S1)
else: total = len(S2)
S1_ranked_list = []
S2_ranked_list = []
for gene in S1:
S1_ranked_list.append((S1[gene].ratio, S1[gene]))
S1_ranked_list.sort()
#S1_ranked_list.reverse()
for gene in S2:
S2_ranked_list.append((S2[gene].ratio, S2[gene]))
S2_ranked_list.sort()
#S2_ranked_list.reverse()
print len(S1_ranked_list), len(S2_ranked_list)
for threshold in xrange(100, 5000, 100):
S1.up = {}
S2.up = {}
for ratio, s1 in S1_ranked_list[:threshold]:
S1.up[s1.id] = s1
for ratio, s2 in S2_ranked_list[:threshold]:
S2.up[s2.id] = s2
Intersection = set(S1.up) & set(S2.up)
pvalue = hyperg(len(S1.up), len(S2.up), total, len(Intersection))
print threshold, '\t', len(S1.up), '\t', len(S2.up), '\t', len(
Intersection
), '\t', pvalue # len(IntersectionUp), pvalueUp, len(S1.down), len(S2.down), len(IntersectionDown), pvalueDown, len(IntersectionComb), pvalueComb
def enriched(self, S1, S2, ratio=1.0, upper=None, step=0.1, pvalue=None):
"""Compares two signatures for significant overlap."""
if isinstance(S1, str): S1 = self[S1] # if only the name is given
if isinstance(S2, str):
S2 = self[S2] # the signature will be identfied
if len(S1) > len(S2): total = len(S1)
else: total = len(S2)
if not upper: upper = 99
Range = arange(ratio, upper, step).tolist()
for upper in Range:
lower = 1 / upper
S1.delta, S1.up, S1.down = {}, {}, {}
S2.delta, S2.up, S2.down = {}, {}, {}
for gene in S1:
if S1[gene].ratio > upper: #or not S1[gene].ratio:
if pvalue:
if S1[gene].pvalue < pvalue: S1.up[gene] = S1[gene]
else: S1.up[gene] = S1[gene]
for gene in S2:
if S2[gene].ratio > upper or not S2[gene].ratio:
if pvalue:
if S2[gene].pvalue < pvalue: S2.up[gene] = S2[gene]
else: S2.up[gene] = S2[gene]
Intersection = set(S1.up) & set(S2.up)
if not S1.up or not S2.up or not Intersection: break
pvalue = hyperg(len(S1.up), len(S2.up), total, len(Intersection))
print upper, len(S1.up), len(
S2.up), len(Intersection), pvalue, ', '.join(Intersection)
def enriched(self, S1, S2, ratio=1.0, upper=None, step=0.1, pvalue=None):
"""Compares two signatures for significant overlap."""
if isinstance(S1, str):
S1 = self[S1] # if only the name is given
if isinstance(S2, str):
S2 = self[S2] # the signature will be identfied
if len(S1) > len(S2):
total = len(S1)
else:
total = len(S2)
if not upper:
upper = 99
Range = arange(ratio, upper, step).tolist()
for upper in Range:
lower = 1 / upper
S1.delta, S1.up, S1.down = {}, {}, {}
S2.delta, S2.up, S2.down = {}, {}, {}
for gene in S1:
if S1[gene].ratio > upper: # or not S1[gene].ratio:
if pvalue:
if S1[gene].pvalue < pvalue:
S1.up[gene] = S1[gene]
else:
S1.up[gene] = S1[gene]
for gene in S2:
if S2[gene].ratio > upper or not S2[gene].ratio:
if pvalue:
if S2[gene].pvalue < pvalue:
S2.up[gene] = S2[gene]
else:
S2.up[gene] = S2[gene]
Intersection = set(S1.up) & set(S2.up)
if not S1.up or not S2.up or not Intersection:
break
pvalue = hyperg(len(S1.up), len(S2.up), total, len(Intersection))
print upper, len(S1.up), len(S2.up), len(Intersection), pvalue, ", ".join(Intersection)
def compare(self, S1, S2, lower=1, upper=99, step=0.1):
"""Compares two signatures for significant overlap."""
if isinstance(S1, str):
S1 = self[S1] # if only the name is given
if isinstance(S2, str):
S2 = self[S2] # the signature will be identfied
## O = Organisms[S.taxid].number_genes
# if S1.type != 'profile' and S2.type != profile:
if len(S1) > len(S2):
total = len(S1)
else:
total = len(S2)
# total = 6600
Range = arange(lower, upper, step).tolist()
for upper in Range:
lower = 1 / upper
## if S1.type == 'profile':
S1.delta = {}
S1.up = {}
S1.down = {}
for s1 in S1:
if S1[s1].ratio > upper or not S1[s1].ratio: # or S1[s1].ratio < lower:
S1.delta[s1] = S1[s1]
## if S1.genes[s1].fold_change > upper:
## S1.up[s1] = S1.genes[s1]
## else:
## S1.down[s1] = S1.genes[s1]
## else:S1.delta = S1.genes
## if S2.type == 'profile':
S2.delta = {}
S2.up = {}
S2.down = {}
for s2 in S2:
# print s2, type(s2), S2[s2].fold_change, hasattr(S2[s2], 'fold_change')
if S2[s2].ratio > upper or not S2[s2].ratio: # S2[s2].ratio < lower:
S2.delta[s2] = S2[s2]
## if S2.genes[s2].fold_change > upper:
## S2.up[s2] = S2.genes[s2]
## else:
## S2.down[s2] = S2.genes[s2]
## else: S2.delta = S2.genes
# print len(S1.delta), len(S2.delta)
Intersection = set(S1.delta) & set(S2.delta)
## IntersectionUp = set(S1.up) & set(S2.up)
## IntersectionDown = set(S1.down) & set(S2.down)
## IntersectionComb = set(IntersectionUp) | set(IntersectionDown)
if not len(S1.delta) or not len(S2.delta) or not Intersection:
return None
pvalue = hyperg(len(S1.delta), len(S2.delta), total, len(Intersection))
## pvalueComb = hyperg(len(S1.delta), len(S2.delta), total, len(IntersectionComb))
## pvalueUp = hyperg(len(S1.up), len(S2.up), total, len(IntersectionUp))
## pvalueDown = hyperg(len(S1.down), len(S2.down), total, len(IntersectionDown))
print upper, "\t", len(S1.delta), "\t", len(S2.delta), "\t", len(
Intersection
), "\t", pvalue # len(IntersectionUp), pvalueUp, len(S1.down), len(S2.down), len(IntersectionDown), pvalueDown, len(IntersectionComb), pvalueComb
## if pvalue < 0.05 and pvalue != 0:
## if len(Intersection) == 4:
## for i in Intersection: print S1.genes[i].symbol, S1.genes[i].fold_change
## stop
## print S1.genes[Result[0]].symbol, S2.genes[Result[0]].fold_change
return len(S1.delta.keys()), len(S2.delta.keys()), len(Intersection)
def compare(self, S1, S2, lower=1, upper=99, step=0.1):
"""Compares two signatures for significant overlap."""
if isinstance(S1, str): S1 = self[S1] # if only the name is given
if isinstance(S2, str):
S2 = self[S2] # the signature will be identfied
## O = Organisms[S.taxid].number_genes
#if S1.type != 'profile' and S2.type != profile:
if len(S1) > len(S2): total = len(S1)
else: total = len(S2)
#total = 6600
Range = arange(lower, upper, step).tolist()
for upper in Range:
lower = 1 / upper
## if S1.type == 'profile':
S1.delta = {}
S1.up = {}
S1.down = {}
for s1 in S1:
if S1[s1].ratio > upper or not S1[
s1].ratio: #or S1[s1].ratio < lower:
S1.delta[s1] = S1[s1]
## if S1.genes[s1].fold_change > upper:
## S1.up[s1] = S1.genes[s1]
## else:
## S1.down[s1] = S1.genes[s1]
## else:S1.delta = S1.genes
## if S2.type == 'profile':
S2.delta = {}
S2.up = {}
S2.down = {}
for s2 in S2:
#print s2, type(s2), S2[s2].fold_change, hasattr(S2[s2], 'fold_change')
if S2[s2].ratio > upper or not S2[
s2].ratio: #S2[s2].ratio < lower:
S2.delta[s2] = S2[s2]
## if S2.genes[s2].fold_change > upper:
## S2.up[s2] = S2.genes[s2]
## else:
## S2.down[s2] = S2.genes[s2]
## else: S2.delta = S2.genes
#print len(S1.delta), len(S2.delta)
Intersection = set(S1.delta) & set(S2.delta)
## IntersectionUp = set(S1.up) & set(S2.up)
## IntersectionDown = set(S1.down) & set(S2.down)
## IntersectionComb = set(IntersectionUp) | set(IntersectionDown)
if not len(S1.delta) or not len(S2.delta) or not Intersection:
return None
pvalue = hyperg(len(S1.delta), len(S2.delta), total,
len(Intersection))
## pvalueComb = hyperg(len(S1.delta), len(S2.delta), total, len(IntersectionComb))
## pvalueUp = hyperg(len(S1.up), len(S2.up), total, len(IntersectionUp))
## pvalueDown = hyperg(len(S1.down), len(S2.down), total, len(IntersectionDown))
print upper, '\t', len(S1.delta), '\t', len(S2.delta), '\t', len(
Intersection
), '\t', pvalue # len(IntersectionUp), pvalueUp, len(S1.down), len(S2.down), len(IntersectionDown), pvalueDown, len(IntersectionComb), pvalueComb
## if pvalue < 0.05 and pvalue != 0:
## if len(Intersection) == 4:
## for i in Intersection: print S1.genes[i].symbol, S1.genes[i].fold_change
## stop
## print S1.genes[Result[0]].symbol, S2.genes[Result[0]].fold_change
return len(S1.delta.keys()), len(S2.delta.keys()), len(Intersection)
