def weighted_motif_stats(mfinderi, motif_stats, stoufferIDs, fweight,
allmotifs):
results = cmfinder.motif_participation(mfinderi)
CI = {}
r_l = results.l
members = cmfinder.intArray(mfinderi.MotifSize)
while (r_l != None):
motif = cmfinder.get_motif(r_l.p)
id = int(motif.id)
idx = 0
CI[id] = np.zeros(motif_stats.motifs[id].real)
am_l = motif.all_members.l
while (am_l != None):
cmfinder.get_motif_members(am_l.p, members, mfinderi.MotifSize)
py_members = [int(members[i]) for i in xrange(mfinderi.MotifSize)]
weight = fweight([
motif_stats.links[x].weight
for x in permutations(py_members, 2) if x in motif_stats.links
])
CI[id][idx] = weight
idx += 1
am_l = am_l.next
r_l = r_l.next
cmfinder.res_tbl_mem_free_single(results)
for motif_id in motif_stats.motifs:
if motif_stats.motifs[motif_id].real > 0:
motif_stats.motifs[motif_id].mean_weight, motif_stats.motifs[
motif_id].sd_weight, motif_stats.motifs[
motif_id].median_weight, motif_stats.motifs[
motif_id].thirdq_weight, motif_stats.motifs[
motif_id].firstq_weight = confidence_interval(
CI[motif_id])
if stoufferIDs:
motif_stats.use_stouffer_IDs()
return motif_stats
def role_stats(mfinderi, roles, links, networktype, stoufferIDs, allroles,
fweight):
results = cmfinder.motif_participation(mfinderi)
possible_roles = set([])
actual_roles = set([])
if networktype == "unipartite":
for m, r in UNIPARTITE_ROLES[mfinderi.MotifSize]:
possible_roles.update([tuple([m] + list(x)) for x in r])
elif networktype == "bipartite":
for m, r in BIPARTITE_ROLES[mfinderi.MotifSize]:
possible_roles.update([tuple([m] + list(x)) for x in r])
if links:
possible_linkroles = set([])
actual_linkroles = set([])
if networktype == "unipartite":
for m, l in UNIPARTITE_LINKS_ROLES[mfinderi.MotifSize]:
possible_linkroles.update([tuple([m] + list(x)) for x in l])
elif networktype == "bipartite":
for m, l in BIPARTITE_LINKS_ROLES[mfinderi.MotifSize]:
possible_linkroles.update([tuple([m] + list(x)) for x in l])
r_l = results.l
members = cmfinder.intArray(mfinderi.MotifSize)
while (r_l != None):
motif = cmfinder.get_motif(r_l.p)
id = int(motif.id)
am_l = motif.all_members.l
while (am_l != None):
cmfinder.get_motif_members(am_l.p, members, mfinderi.MotifSize)
py_members = [int(members[i]) for i in xrange(mfinderi.MotifSize)]
py_motif = [
x for x in permutations(py_members, 2) if x in roles.links
]
if roles.weighted:
weight_motif = fweight(
[roles.links[x].weight for x in py_motif])
weight_i = [
fweight([
roles.links[x].weight for x in py_motif
if x[0] == m or x[1] == m
]) for m in py_members
]
weight = weight_motif / float(sum(weight_i))
for idm, m in enumerate(py_members):
npred, nprey = 0, 0
for othernode in py_members:
if (othernode, m) in py_motif:
npred += 1
if (m, othernode) in py_motif:
nprey += 1
key = (id, npred, nprey)
# if the node's in and out degrees are insufficient to discern its role
# we will add the degrees of the nodes it interacts with (its neighbors)
if key not in possible_roles:
if npred > 0:
connected_to = set([
othernode for othernode in py_members
if othernode != m and (othernode, m) in py_motif
])
npreys = [
sum([(i, j) in py_motif for j in py_members
if j != i]) for i in connected_to
]
npreys.sort()
key = tuple(list(key) + [tuple(npreys)])
else:
connected_to = set([
othernode for othernode in py_members
if othernode != m and (m, othernode) in py_motif
])
npreds = [
sum([(j, i) in py_motif for j in py_members
if j != i]) for i in connected_to
]
npreds.sort()
key = tuple(list(key) + [tuple(npreds)])
if key not in possible_roles:
print >> sys.stderr, key
print >> sys.stderr, "Apparently there is a role you aren't accounting for in roles.py."
sys.exit()
try:
roles.nodes[m].roles[key] += 1
except KeyError:
roles.nodes[m].roles[key] = 1
if roles.weighted:
try:
roles.nodes[m].weighted_roles[
key] += weight_i[idm] * weight
except KeyError:
roles.nodes[m].weighted_roles[
key] = weight_i[idm] * weight
actual_roles.add(key)
if links:
for n in py_members:
if n != m and (n, m) in roles.links:
npred1, npred2, nprey1, nprey2 = 0, 0, 0, 0
for othernode in py_members:
if (othernode, n) in py_motif:
npred1 += 1
if (n, othernode) in py_motif:
nprey1 += 1
if (othernode, m) in py_motif:
npred2 += 1
if (m, othernode) in py_motif:
nprey2 += 1
key = (id, (npred1, nprey1), (npred2, nprey2))
if key not in possible_linkroles:
key = (id, (npred2, nprey2), (npred1, nprey1))
if key not in possible_linkroles:
print >> sys.stderr, key
print >> sys.stderr, "Apparently there is a role you aren't accounting for in roles.py."
try:
roles.links[(n, m)].roles[key] += 1
except KeyError:
roles.links[(n, m)].roles[key] = 1
if roles.weighted:
try:
roles.links[(
n,
m)].weighted_roles[key] += weight_motif
except KeyError:
roles.links[(
n,
m)].weighted_roles[key] = weight_motif
actual_linkroles.add(key)
am_l = am_l.next
r_l = r_l.next
cmfinder.res_tbl_mem_free_single(results)
if not allroles:
possible_roles = actual_roles
if links:
possible_linkroles = actual_linkroles
for n in roles.nodes:
for r in possible_roles:
try:
x = roles.nodes[n].roles[r]
except KeyError:
roles.nodes[n].roles[r] = 0
if roles.weighted:
try:
x = roles.nodes[n].weighted_roles[r]
except KeyError:
roles.nodes[n].weighted_roles[r] = 0
if links:
for n in roles.links:
for r in possible_linkroles:
try:
x = roles.links[n].roles[r]
except KeyError:
roles.links[n].roles[r] = 0
if roles.weighted:
try:
x = roles.links[n].weighted_roles[r]
except KeyError:
roles.links[n].weighted_roles[r] = 0
if stoufferIDs:
roles.use_stouffer_IDs()
return roles
def participation_stats(mfinderi, participation, links, stoufferIDs, allmotifs,
fweight):
results = cmfinder.motif_participation(mfinderi)
r_l = results.l
members = cmfinder.intArray(mfinderi.MotifSize)
while (r_l != None):
motif = cmfinder.get_motif(r_l.p)
id = int(motif.id)
am_l = motif.all_members.l
while (am_l != None):
cmfinder.get_motif_members(am_l.p, members, mfinderi.MotifSize)
py_members = [int(members[i]) for i in xrange(mfinderi.MotifSize)]
if participation.weighted:
weight = fweight([
participation.links[x].weight
for x in permutations(py_members, 2)
if x in participation.links
])
for m in py_members:
try:
participation.nodes[m].motifs[id] += 1
except KeyError:
participation.nodes[m].motifs[id] = 1
try:
participation.nodes[m].weighted_motifs[id] += weight
except KeyError:
participation.nodes[m].weighted_motifs[id] = weight
else:
for m in py_members:
try:
participation.nodes[m].motifs[id] += 1
except KeyError:
participation.nodes[m].motifs[id] = 1
if links:
for m in permutations(py_members, 2):
if m in participation.links:
try:
participation.links[m].motifs[id] += 1
except KeyError:
participation.links[m].motifs[id] = 1
if participation.weighted:
try:
participation.links[m].weighted_motifs[
id] += weight
except KeyError:
participation.links[m].weighted_motifs[
id] = weight
am_l = am_l.next
r_l = r_l.next
cmfinder.res_tbl_mem_free_single(results)
possible_motifs = set(participation.motifs.keys())
for r in possible_motifs:
for n in participation.nodes:
try:
x = participation.nodes[n].motifs[r]
except KeyError:
participation.nodes[n].motifs[r] = 0
if participation.weighted:
try:
x = participation.nodes[n].weighted_motifs[r]
except KeyError:
participation.nodes[n].weighted_motifs[r] = 0
if links:
for n in participation.links:
try:
x = participation.links[n].motifs[r]
except KeyError:
participation.links[n].motifs[r] = 0
if participation.weighted:
try:
x = participation.links[n].weighted_motifs[r]
except KeyError:
participation.links[n].weighted_motifs[r] = 0
if stoufferIDs:
participation.use_stouffer_IDs()
return participation