def net_ggsvd(name=nu.default_name, reset=0):
hardcopy = False
try:
if reset:
raise Exception("compute")
return nw.readnet(name, hardcopy=hardcopy)
except Exception as e:
if e.args[0] != "compute":
raise Exception()
nw.claim_reset()
ggn = nu.net_genegene_norm(reset=mod(reset, 2))
U, S, Vh = lin.svd(ggn)
V = Vh.T
dosave = (U, S, V)
nw.writenet(name, dosave, hardcopy=hardcopy)
print """
Ran ggsvd.
No hardcopies have been saved yet"""
if reset:
net_ggsvd_U(reset=2)
net_ggsvd_V(reset=2)
net_ggsvd_S(reset=2)
print """
...saved hardcopies of U,S,V
"""
return dosave
def net_square_svd(name=nu.default_name, reset=0):
hardcopy = False
try:
if reset:
raise Exception("compute")
return nw.readnet(name, hardcopy=hardcopy)
except Exception as e:
if e.args[0] != "compute":
raise Exception()
nw.claim_reset()
sqa = nu.net_square_affinity(reset=mod(reset, 2))
U, S, Vh = lin.svd(sqa)
V = Vh.T
uvecs = U[:, : len(S)]
vvecs = V
dosave = (sqa[1], (uvecs, S, vvecs))
nw.writenet(name, dosave, hardcopy=hardcopy)
print """
Ran net square svd for the current values.
Nothing has yet been saved to HD.
"""
if reset:
net_square_svd_U(reset=2)
net_square_svd_V(reset=2)
net_square_svd_S(reset=2)
print """
...saved hardcopies of U,S,V
"""
return dosave
def get_net(name = 'unsup' , reset = 0):
hardcopy = True
try:
if reset: raise Exception('compute')
return nw.readnet(name, hardcopy = hardcopy)
except Exception, e:
if e.args[0] != 'compute': raise Exception()
nw.claim_reset()
net = parse_name(name)
nw.writenet(name, net, hardcopy = hardcopy)
return net
def net_cluster_ggsvdV(k = k,reset = 0):
hardcopy = True
try:
if reset: raise Exception('compute')
out,sxs = nw.rn2(name, hardcopy = hardcopy)
if not sxs: raise Exception()
except Exception as e:
if e.args[0] != 'compute': raise Exception()
nw.claim_reset()
gg = ns.net_ggsvd_V().T
kmeans = mlpy.Kmeans(k)
clustered = kmeans.compute(gg[0:maxgenes,:])
means = kmeans.means
nw.wn2(name, (clustered, means) ,hardcopy = hardcopy)
return out
def net_cluster_genes_by_tf(k= k, reset = 0):
hardcopy = True
try:
if reset: raise Exception('compute')
out,sxs = nw.rn2(name, hardcopy = hardcopy)
if not sxs: raise Exception()
except Exception as e:
if e.args[0] != 'compute': raise Exception()
nw.claim_reset()
gg = nu.net_affinity(reset = mod(reset,2))
kmeans = mlpy.Kmeans(k)
clustered = kmeans.compute(gg[0:maxgenes,:])
means = kmeans.means
out = (clustered,means)
nw.wn2(name, (clustered, means) ,hardcopy = hardcopy)
return out
def net_svd(name=nu.default_name, reset=0):
hardcopy = True
try:
if reset:
raise Exception("compute")
return nw.readnet(name=nu.default_name, hardcopy=hardcopy)
except Exception as e:
if e.args[0] != "compute":
raise Exception()
nw.claim_reset()
a = nu.net_affinity(reset=mod(reset, 2))[0]
N = a[0]
U, S, Vh = lin.svd(N)
V = Vh.T
U = U[:, len(S)]
dosave = (a[1], (U, S, V))
nw.writenet(name, dosave, hardcopy=hardcopy)
return dosave