def q4(cube, pyramid, show=False):
matriz_projecao = [[1, 0, 0], [0, 1, 0], [0, 0, 0]]
fig = plt.figure()
ax = fig.add_subplot(111)
cube_faces = get_rectangle_faces(np.dot(cube, matriz_projecao))
arestas = get_edges(cube_faces)
arestas = iterable_to_list(arestas)
for aresta in arestas:
aresta = np.array(aresta)
ax.plot(aresta[:, 0], aresta[:, 1], color='blue')
cube_faces = get_triangle_faces(np.dot(pyramid, matriz_projecao))
arestas = get_edges(cube_faces)
arestas = iterable_to_list(arestas)
for aresta in arestas:
aresta = np.array(aresta)
ax.plot(aresta[:, 0], aresta[:, 1], color='red')
plt.gca().set_aspect('equal')
ax.set_xlim([-6, 6])
ax.set_ylim([-6, 6])
if show:
plt.show()
else:
plt.savefig(ROOT_DIR / 'gif_images' / (str(datetime.now()) + ".png"))
def create_graph_weights(nodeweights, fname):
positions = pk.load(open("county_locations.dict"))
positions = sorted(positions.items(), key=lambda (k, v) : k)
positions = map(lambda (k, v) : (v[1], v[0]), positions)
names = utils.get_name_map("../mississippi_county.list")
edges = utils.get_edges("../mississippi_graph_NS.csv", names)
g = Graph()
g.set_directed(True)
vertices = g.add_vertex(len(names))
cap = g.new_edge_property("double")
pos = g.new_vertex_property("vector<double>")
colors = g.new_vertex_property("vector<double>")
for i in range(len(nodeweights)):
colors[i] = color_from_weight(nodeweights[i])
for p in range(len(positions)):
(x, y) = positions[p]
pos[p] = [x, -y]
for e in edges:
edge = g.add_edge(e[0], e[1])
cap[edge] = e[2]
graph_draw(g, pos=pos, edge_pen_width=prop_to_size(cap, mi=1, ma=10, power=1),
vertex_fill_color=colors,
vertex_text=g.vertex_index,
vertex_font_size=15, output=fname,
fit_view=True, output_size=(800, 1200))
def route_datasets(request):
routes = get_routes(SOURCE, DESTINATION)
#print routes
try:
route = routes[int(request.GET.get("route_index"))]
except:
route = routes[0]
edges = get_edges(route)
#route = [1, 2, 5, 4, 7, 6, 3, 9, 8, 10]
#edges = get_edges_by_index(route)
#edges = Edge.objects.all()[:5]
edges = serialize('geojson', edges)
return HttpResponse(edges, content_type='json')
def build_rules():
""" Actin network rules.
Changes from initial model:
* direct activation link RhoA -> Rac1
* ROCK inhibition delay: RhoA -> ROCK -> ROCK_ -| Rac1
* weaker RhoA inhibition rule: not Rac1 or not PAK
Changes from v1:
* strong inhibitors for Arp2_3 (reworked voting rule)
* reworked rule for Cortactin
Changes from v2:
* deleted PKD activates PAK
* added link PKD activates LIMK
* Option A: deleted PAK -> Cortactin link
* deleted IRSp53 -> WAVE link
* deleted Rac1 -> IRSp53 link
Changes from v3:
* separate IRSp53 variants Cdc42 and Rac1 activations
"""
UPSTREAM = "UPSTREAM"
G = nx.DiGraph()
rules = ""
rules += "1: UPSTREAM* = not UPSTREAM \n"
G.add_weighted_edges_from(
get_edges(WASP, [Rac1, Cdc42, PIP2, Cortactin, IRSp53_Cdc42],
[Thymosin]))
rules += "1: WASP* = not Thymosin and (Rac1 or Cdc42 or PIP2 or Cortactin or IRSp53_Cdc42) \n"
G.add_weighted_edges_from(get_edges(WAVE, [Rac1, IRSp53_Rac1], []))
rules += "1: WAVE* = Rac1 or IRSp53_Rac1 \n"
G.add_weighted_edges_from(
get_edges(Arp2_3, [PAK, WASP, WAVE, Cortactin],
[Profilin, Thymosin, Coronin]))
rules += "1: Arp2_3* = PAK and (" + voting_rule(
[WASP, WAVE, Cortactin], [Profilin, Thymosin, Coronin]) + ")\n"
G.add_weighted_edges_from(get_edges(Rac1, [UPSTREAM], []))
rules += "1: Rac1* = UPSTREAM \n"
G.add_weighted_edges_from(get_edges(RhoA, [], [UPSTREAM]))
rules += "1: RhoA* = not UPSTREAM \n"
G.add_weighted_edges_from(get_edges(Thymosin, [], [WASP, Cofilin]))
rules += "1: Thymosin* = (not WASP and not Cofilin) \n"
G.add_weighted_edges_from(get_edges(Cortactin, [Rac1], [Coronin, PKD]))
rules += "1: Cortactin* = " + voting_rule([Rac1], [Coronin, PKD]) + " \n"
G.add_weighted_edges_from(get_edges(IRSp53_Cdc42, [Cdc42], []))
rules += "1: IRSp53_Cdc42* = Cdc42 \n"
G.add_weighted_edges_from(get_edges(IRSp53_Rac1, [Rac1], []))
rules += "1: IRSp53_Rac1* = Rac1 \n"
G.add_weighted_edges_from(get_edges(PAK, [Rac1, Cdc42], []))
rules += "1: PAK* = Rac1 or Cdc42 \n"
G.add_weighted_edges_from(get_edges(Dia1, [RhoA], [CP]))
rules += "1: Dia1* = RhoA and not CP \n"
G.add_weighted_edges_from(get_edges(Dia2, [Rac1, RhoA], []))
rules += "1: Dia2* = Rac1 or RhoA \n"
G.add_weighted_edges_from(
get_edges(Ena_Vasp, [IRSp53_Cdc42, WASP, PKD], []))
rules += "1: Ena_Vasp* = IRSp53_Cdc42 or WASP or PKD \n"
G.add_weighted_edges_from(
get_edges(Profilin, [WASP, Dia1, WAVE], [Thymosin, PIP2]))
rules += "1: Profilin* = " + voting_rule(["WASP", "Dia1", "WAVE"],
["Thymosin", "PIP2"]) + " \n"
G.add_weighted_edges_from(get_edges(CP, [Arp2_3], [Ena_Vasp, PIP2]))
rules += "1: CP* = (Arp2_3 and not Ena_Vasp) or not PIP2 \n"
G.add_weighted_edges_from(get_edges(Coronin, [SSH], []))
rules += "1: Coronin* = SSH \n"
G.add_weighted_edges_from(get_edges(ROCK, [RhoA], [SSH, Coronin]))
rules += "1: ROCK* = RhoA and not (SSH and Coronin) \n"
G.add_weighted_edges_from(get_edges(PKD, [ROCK], []))
rules += "1: PKD* = ROCK \n"
G.add_weighted_edges_from(get_edges(LIMK, [ROCK, PAK, PKD], [SSH]))
rules += "1: LIMK* = (ROCK or PAK or PKD) and not SSH \n"
G.add_weighted_edges_from(
get_edges(Cofilin, [SSH, Arp2_3], [PIP2, Thymosin, LIMK, Cortactin]))
rules += "1: Cofilin* = " + voting_rule(
["SSH", "Arp2_3"], ["PIP2", "Thymosin", "LIMK", "Cortactin"]) + "\n"
G.add_weighted_edges_from(get_edges(SSH, [Coronin, Rac1], [PKD]))
rules += "1: SSH* = (Coronin or Rac1) and not PKD \n"
G.add_weighted_edges_from(get_edges(Actin_BR, [Arp2_3], []))
rules += "1: Actin_BR* = Arp2_3 \n"
G.add_weighted_edges_from(
get_edges(Actin_ST, [Profilin, Dia1, Dia2, Ena_Vasp], [CP, Cofilin]))
rules += "1: Actin_ST* = Profilin and (" + voting_rule(
["Dia1", "Dia2", "Ena_Vasp"], ["CP", "Cofilin"]) + ")\n"
return {"rules": rules, "graph": G}
import utils
from graph_tool.all import *
import graph_tool.flow as gt
import pickle as pk
if __name__ == "__main__":
positions = pk.load(open("county_locations.dict"))
positions = sorted(positions.items(), key=lambda (k, v): k)
positions = map(lambda (k, v): (v[1], v[0]), positions)
names = utils.get_name_map("../mississippi_county.list")
edges = utils.get_edges("../mississippi_graph_NS.csv", names)
# edges += utils.get_edges("../mississippi_graph_EW.csv", names)
g = Graph()
g.set_directed(True)
vertices = g.add_vertex(len(names))
cap = g.new_edge_property("double")
pos = g.new_vertex_property("vector<double>")
for p in range(len(positions)):
(x, y) = positions[p]
pos[p] = [x, -y]
for e in edges:
edge = g.add_edge(e[0], e[1])
cap[edge] = e[2]
graph_draw(
g,
from graph import Graph
import utils
if __name__ == "__main__":
v, adjacency_matrix = utils.read_from_file("matrix")
edges = utils.get_edges(adjacency_matrix)
g = Graph(v)
utils.add_edges(g, edges)
g.dfs(2)
print("-----------------------------")
g1 = Graph(v)
utils.add_edges(g1, edges)
g1.bfs(4)
print("-----------------------------")
def build_rules():
""" Actin network rules.
Changes from initial model:
* direct activation link RhoA -> Rac1
* ROCK inhibition delay: RhoA -> ROCK -> ROCK_ -| Rac1
* weaker RhoA inhibition rule: not Rac1 or not PAK
Changes from v1:
* strong inhibitors for Arp2_3 (reworked voting rule)
* reworked rule for Cortactin
"""
Actin_BR = "Actin_BR"
Actin_ST = "Actin_ST"
Arp2_3 = "Arp2_3"
CP = "CP"
Cdc42 = "Cdc42"
Cofilin = "Cofilin"
Coronin = "Coronin"
Cortactin = "Cortactin"
Dia1 = "Dia1"
Dia2 = "Dia2"
Ena_Vasp = "Ena_Vasp"
IRSp53 = "IRSp53"
LIMK = "LIMK"
PAK = "PAK"
PIP2 = "PIP2"
PKD = "PKD"
Profilin = "Profilin"
ROCK = "ROCK"
ROCK_ = "ROCK_"
Rac1 = "Rac1"
RhoA = "RhoA"
SSH = "SSH"
Thymosin = "Thymosin"
WASP = "WASP"
WAVE = "WAVE"
G = nx.DiGraph()
rules = ""
G.add_weighted_edges_from(
get_edges(WASP, [Rac1, Cdc42, PIP2, Cortactin, IRSp53], [Thymosin]))
rules += "1: WASP* = not Thymosin and (Rac1 or Cdc42 or PIP2 or Cortactin or IRSp53) \n"
G.add_weighted_edges_from(get_edges(WAVE, [Rac1], []))
rules += "1: WAVE* = Rac1 \n" # or IRSp53
G.add_weighted_edges_from(
get_edges(Arp2_3, [PAK, WASP, WAVE, Cortactin],
[Profilin, Thymosin, Coronin]))
rules += "1: Arp2_3* = PAK and (" + voting_rule(
[WASP, WAVE, Cortactin], [Profilin, Thymosin, Coronin],
strongInhibition=False) + ")\n"
G.add_weighted_edges_from(get_edges(Rac1, [Arp2_3, Dia1, RhoA], [ROCK_]))
rules += "1: Rac1* = not ROCK_ and (Arp2_3 or Dia1 or RhoA) \n" # intermediate ROCK_ node + activation from RhoA
G.add_weighted_edges_from(get_edges(RhoA, [], [Rac1, PAK]))
rules += "1: RhoA* = not Rac1 or not PAK \n"
G.add_weighted_edges_from(get_edges(Thymosin, [], [WASP, Cofilin]))
rules += "1: Thymosin* = not WASP and not Cofilin \n"
G.add_weighted_edges_from(get_edges(Cortactin, [Rac1, PAK],
[Coronin, PKD]))
rules += "1: Cortactin* = (Rac1 and PAK) or (Rac1 and not (Coronin and PKD) ) \n"
# rules += "1: Cortactin* = (Rac1 and not (Coronin and PKD) \n"
G.add_weighted_edges_from(get_edges(IRSp53, [Cdc42, Rac1], []))
rules += "1: IRSp53* = Cdc42 or Rac1 \n"
G.add_weighted_edges_from(get_edges(PAK, [Rac1, Cdc42, PKD], []))
rules += "1: PAK* = Rac1 or Cdc42 or PKD \n"
G.add_weighted_edges_from(get_edges(Dia1, [RhoA], [CP]))
rules += "1: Dia1* = RhoA and not CP \n"
G.add_weighted_edges_from(get_edges(Dia2, [Rac1, RhoA], []))
rules += "1: Dia2* = Rac1 or RhoA \n"
G.add_weighted_edges_from(get_edges(Ena_Vasp, [IRSp53, WASP, PKD], []))
rules += "1: Ena_Vasp* = IRSp53 or WASP or PKD \n"
G.add_weighted_edges_from(
get_edges(Profilin, [WASP, Dia1, WAVE], [Thymosin, PIP2]))
rules += "1: Profilin* = " + voting_rule(["WASP", "Dia1", "WAVE"],
["Thymosin", "PIP2"]) + " \n"
G.add_weighted_edges_from(get_edges(CP, [Arp2_3], [Ena_Vasp, PIP2]))
rules += "1: CP* = (Arp2_3 and not Ena_Vasp) or not PIP2 \n"
G.add_weighted_edges_from(get_edges(Coronin, [SSH], []))
rules += "1: Coronin* = SSH \n"
G.add_weighted_edges_from(get_edges(ROCK, [RhoA], [SSH, Coronin]))
rules += "1: ROCK* = RhoA and not (SSH and Coronin) \n"
G.add_weighted_edges_from(get_edges(ROCK_, [ROCK], []))
rules += "1: ROCK_* = ROCK \n"
G.add_weighted_edges_from(get_edges(PKD, [ROCK], []))
rules += "1: PKD* = ROCK \n"
G.add_weighted_edges_from(get_edges(LIMK, [ROCK, PAK], [SSH]))
rules += "1: LIMK* = (ROCK or PAK) and not SSH \n"
G.add_weighted_edges_from(
get_edges(Cofilin, [SSH, Arp2_3], [PIP2, Thymosin, LIMK, Cortactin]))
rules += "1: Cofilin* = " + voting_rule(
["SSH", "Arp2_3"], ["PIP2", "Thymosin", "LIMK", "Cortactin"]) + "\n"
G.add_weighted_edges_from(get_edges(SSH, [Coronin, Rac1], [PKD]))
rules += "1: SSH* = (Coronin or Rac1) and not PKD \n"
G.add_weighted_edges_from(get_edges(Actin_BR, [Arp2_3], []))
rules += "1: Actin_BR* = (Arp2_3) \n" # or Cofilin) and not Thymosin
G.add_weighted_edges_from(
get_edges(Actin_ST, [Profilin, Dia1, Dia2, Ena_Vasp], [CP, Cofilin]))
rules += "1: Actin_ST* = Profilin and (" + voting_rule(
["Dia1", "Dia2", "Ena_Vasp"], ["CP", "Cofilin"]) + ")\n"
return {"rules": rules, "graph": G}
cnets_masks[i][j] = tmp
print('cross_network mask done')
#print(maskes[0])
dmgc = DMGC(dims=config, n_clusters=n_clusters, init=glorot)
print('build model done')
u_is = []
u_js = []
u_labels = []
for i in range(n_networks):
G = Gs[i]
u_i, u_j, u_label = get_edges(G)
u_is.append(u_i)
u_js.append(u_j)
u_labels.append(u_label)
print('prepare to feed data')
dmgc.feedData(adjs,
maskes,
xs,
cnets,
cnets_masks,
u_js=u_js,
u_is=u_is,
u_labels=u_labels)
print('feed data done')
def build_rules():
""" Example network rules for validation.
"""
egf = "egf"
nrg1 = "nrg1"
erbb1 = "erbb1"
erbb2 = "erbb2"
erbb3 = "erbb3"
erbb11 = "erbb11"
erbb13 = "erbb13"
erbb23 = "erbb23"
grb2 = "grb2"
gab1 = "gab1"
pi3k = "pi3k"
sos = "sos"
ras = "ras"
mek = "mek"
erk = "erk"
pip3 = "pip3"
akt = "akt"
G = nx.DiGraph()
rules = ""
G.add_weighted_edges_from(get_edges(erbb11, [egf, erbb1], []))
rules += "1: erbb11* = egf and erbb1\n"
G.add_weighted_edges_from(
get_edges(erbb13, [egf, erbb1, erbb3, nrg1], [erbb2]))
rules += "1: erbb13* = (egf and erbb1 and not erbb2 and erbb3) or (erbb1 and not erbb2 and erbb3 and nrg1) \n"
G.add_weighted_edges_from(get_edges(erbb23, [erbb2, erbb3, nrg1], []))
rules += "1: erbb23* = erbb2 and erbb3 and nrg1 \n"
G.add_weighted_edges_from(get_edges(grb2, [erbb11, erbb13, erbb23], []))
rules += "1: grb2* = erbb11 or erbb13 or erbb23\n"
G.add_weighted_edges_from(get_edges(gab1, [grb2, pip3], []))
rules += "1: gab1* = grb2 and pip3 \n"
G.add_weighted_edges_from(get_edges(pi3k, [erbb13, erbb23, gab1, ras], []))
rules += "1: pi3k* = erbb13 or erbb23 or gab1 or ras \n"
G.add_weighted_edges_from(get_edges(sos, [grb2], [erk]))
rules += "1: sos* = grb2 and not erk\n"
G.add_weighted_edges_from(get_edges(ras, [sos], []))
rules += "1: ras* = sos\n"
G.add_weighted_edges_from(get_edges(mek, [ras], []))
rules += "1: mek* = ras\n"
G.add_weighted_edges_from(get_edges(erk, [mek], []))
rules += "1: erk* = mek\n"
G.add_weighted_edges_from(get_edges(pip3, [pi3k], []))
rules += "1: pip3* = pi3k\n"
G.add_weighted_edges_from(get_edges(akt, [pip3], []))
rules += "1: akt* = pip3\n"
return {"rules": rules, "graph": G}
def build_rules():
""" Original Actin network rules.
"""
Actin_BR = "Actin_BR"
Actin_ST = "Actin_ST"
Arp2_3 = "Arp2_3"
CP = "CP"
Cdc42 = "Cdc42"
Cofilin = "Cofilin"
Coronin = "Coronin"
Cortactin = "Cortactin"
Dia1 = "Dia1"
Dia2 = "Dia2"
Ena_Vasp = "Ena_Vasp"
IRSp53 = "IRSp53"
LIMK = "LIMK"
PAK = "PAK"
PIP2 = "PIP2"
PKD = "PKD"
Profilin = "Profilin"
ROCK = "ROCK"
Rac1 = "Rac1"
RhoA = "RhoA"
SSH = "SSH"
Thymosin = "Thymosin"
WASP = "WASP"
WAVE = "WAVE"
G = nx.DiGraph()
rules = ""
G.add_weighted_edges_from(get_edges(WASP, [Rac1, Cdc42, PIP2, Cortactin, IRSp53], [Thymosin]))
rules += "1: WASP* = not Thymosin and (Rac1 or Cdc42 or PIP2 or Cortactin or IRSp53) \n"
G.add_weighted_edges_from(get_edges(WAVE, [Rac1], []))
rules += "1: WAVE* = Rac1 \n" # or IRSp53
G.add_weighted_edges_from(get_edges(Arp2_3, [PAK, WASP, WAVE, Cortactin], [Profilin, Thymosin, Coronin]))
rules += "1: Arp2_3* = PAK and (" + voting_rule([WASP, WAVE, Cortactin],
[Profilin, Thymosin, Coronin]) + ")\n"
G.add_weighted_edges_from(get_edges(Rac1, [Arp2_3, Dia1, RhoA], [ROCK]))
rules += "1: Rac1* = not ROCK and (Arp2_3 or Dia1) \n"
G.add_weighted_edges_from(get_edges(RhoA, [], [Rac1, PAK]))
rules += "1: RhoA* = not Rac1 and not PAK \n"
G.add_weighted_edges_from(get_edges(Thymosin, [], [WASP, Cofilin]))
rules += "1: Thymosin* = not WASP and not Cofilin \n"
G.add_weighted_edges_from(get_edges(Cortactin, [Rac1, PAK], [Coronin, PKD]))
rules += "1: Cortactin* = (Rac1 and PAK) or ((Rac1 or PAK) and not (Coronin and PKD)) \n" # voting
G.add_weighted_edges_from(get_edges(IRSp53, [Cdc42, Rac1], []))
rules += "1: IRSp53* = Cdc42 or Rac1 \n"
G.add_weighted_edges_from(get_edges(PAK, [Rac1, Cdc42, PKD], []))
rules += "1: PAK* = Rac1 or Cdc42 or PKD \n"
G.add_weighted_edges_from(get_edges(Dia1, [RhoA], [CP]))
rules += "1: Dia1* = RhoA and not CP \n"
G.add_weighted_edges_from(get_edges(Dia2, [Rac1, RhoA], []))
rules += "1: Dia2* = Rac1 or RhoA \n"
G.add_weighted_edges_from(get_edges(Ena_Vasp, [IRSp53, WASP, PKD], []))
rules += "1: Ena_Vasp* = IRSp53 or WASP or PKD \n"
G.add_weighted_edges_from(get_edges(Profilin, [WASP, Dia1, WAVE], [Thymosin, PIP2]))
rules += "1: Profilin* = " + voting_rule(["WASP", "Dia1", "WAVE"], ["Thymosin", "PIP2"]) + " \n"
G.add_weighted_edges_from(get_edges(CP, [Arp2_3], [Ena_Vasp, PIP2]))
rules += "1: CP* = (Arp2_3 and not Ena_Vasp) or not PIP2 \n"
G.add_weighted_edges_from(get_edges(Coronin, [SSH], []))
rules += "1: Coronin* = SSH \n"
G.add_weighted_edges_from(get_edges(ROCK, [RhoA], [SSH, Coronin]))
rules += "1: ROCK* = RhoA and not (SSH and Coronin) \n"
G.add_weighted_edges_from(get_edges(PKD, [ROCK], []))
rules += "1: PKD* = ROCK \n"
G.add_weighted_edges_from(get_edges(LIMK, [ROCK, PAK], [SSH]))
rules += "1: LIMK* = (ROCK or PAK) and not SSH \n"
G.add_weighted_edges_from(get_edges(Cofilin, [SSH, Arp2_3], [PIP2, Thymosin, LIMK, Cortactin]))
rules += "1: Cofilin* = " + voting_rule(["SSH", "Arp2_3"],
["PIP2", "Thymosin", "LIMK", "Cortactin"]) + "\n"
G.add_weighted_edges_from(get_edges(SSH, [Coronin, Rac1], [PKD]))
rules += "1: SSH* = (Coronin or Rac1) and not PKD \n"
G.add_weighted_edges_from(get_edges(Actin_BR, [Arp2_3], []))
rules += "1: Actin_BR* = (Arp2_3) \n" # or Cofilin) and not Thymosin
G.add_weighted_edges_from(get_edges(Actin_ST, [Profilin, Dia1, Dia2, Ena_Vasp], [CP, Cofilin]))
rules += "1: Actin_ST* = Profilin and (" + voting_rule(["Dia1", "Dia2", "Ena_Vasp"],
["CP", "Cofilin"]) + ")\n"
return {"rules":rules, "graph":G}
