def plot(self):
pos = nx_drawing.pygraphviz_layout(self.graph, prog='dot')
for k in pos:
x, y = pos[k]
pos[k] = (x, y + np.random.randint(-10, 10))
plt.figure(figsize=(20, 12))
nx.draw(self.graph, pos, with_labels=True, arrows=True, )
plt.show()
def draw(self, subset=None):
if subset is None:
dag = self.dag
else:
dag = self.dag.subgraph(subset)
pos = pygraphviz_layout(dag, prog='dot')
nx.draw(dag, pos, with_labels=True)
plt.show()
def save_graph(self, graph, file_name):
plt.title('draw_networkx')
pos=pygraphviz_layout(graph, prog='dot')
newpos = {}
for k,v in pos.items():
newpos[k] = (k,v[0],v[1])
sorted_by_x = sorted(
list(newpos.values()), key=lambda tup: (tup[2],tup[1]))
rank = []
nodesep = 1000
for k, xx, yy in sorted_by_x:
if yy not in rank:
rank.append(yy)
newpos[k] = (xx, yy)
newxx = xx + nodesep
else:
newpos[k] = (newxx, yy)
newxx += nodesep
nx.draw(graph, newpos, node_size=30, with_labels=False, arrows=True)
plt.savefig(file_name)
plt.close()
def to_hipathia_dfs(
graph: BELGraph,
draw_directory: Optional[str] = None,
) -> Union[Tuple[None, None], Tuple[pd.DataFrame, pd.DataFrame]]:
"""Get the ATT and SIF dataframes.
:param graph: A BEL graph
:param draw_directory: The directory in which a drawing should be output
1. Identify nodes:
1. Identify all proteins
2. Identify all protein families
3. Identify all complexes with just a protein or a protein family in them
2. Identify interactions between any of those things that are causal
3. Profit!
"""
proteins = set()
families = defaultdict(set)
complexes = set()
for node in sorted(graph, key=str):
if isinstance(node, Protein):
children = _is_node_family(graph, node)
if children:
families[node] = children
else:
proteins.add(node)
elif isinstance(node, ComplexAbundance) and all(
isinstance(m, Protein) for m in node.members):
complexes.add(node)
families = {
node: sorted(values, key=str)
for node, values in sorted(families.items(), key=itemgetter(0))
}
nodes = sorted(proteins.union(families).union(complexes), key=str)
new_nodes = set()
edges = []
for u, v, _, d in sorted(graph.out_edges(nodes, keys=True, data=True),
key=lambda t: (str(t[0]), str(t[1]), t[2])):
relation = d[RELATION]
if relation not in CAUSAL_POLAR_RELATIONS:
continue
new_nodes.add(u)
new_nodes.add(v)
edges.append((u, 'activation' if relation in CAUSAL_INCREASE_RELATIONS
else 'inhibition', v))
att = {}
dsl_to_k = {}
i = 0
for node in sorted(new_nodes, key=str):
if node in families:
i += 1
k = (i, )
children = families[node]
child_identifiers = [child.identifier for child in children]
if not all(child_identifiers):
logger.warning('not all children were grounded: %s',
child_identifiers)
continue
labels, genes_lists = [node.name], [child_identifiers]
elif isinstance(node, Protein):
if not node.identifier or not node.name:
logger.warning('node was not grounded: %s', node)
continue
i += 1
k = (i, )
labels, genes_lists = [node.name], [[node.identifier]]
elif isinstance(node, ComplexAbundance):
k, labels, genes_lists = [], [], []
for member in node.members:
i += 1
k.append(i)
labels.append(member.name)
if member in families:
children = families[member]
child_identifiers = [
child.identifier for child in children
]
if not all(child_identifiers):
logger.warning('not all children were grounded: %s',
child_identifiers)
continue
genes_lists.append(child_identifiers)
else:
if not member.identifier:
logger.warning('member was not grounded: %s', member)
continue
genes_lists.append([member.identifier])
k = tuple(k)
else:
logger.debug('skipping node {}'.format(node))
continue
k = 'N-{}-{}'.format(graph.name, ' '.join(map(str, k)))
att[k] = labels, genes_lists
dsl_to_k[node] = k
edges = [(dsl_to_k[source], relation, dsl_to_k[target])
for source, relation, target in edges
if source in dsl_to_k and target in dsl_to_k]
sif_df = pd.DataFrame(edges) # DONE
composite_graph = nx.Graph([(k_source, k_target)
for k_source, _, k_target in edges])
try:
from networkx.drawing.nx_agraph import pygraphviz_layout
pos = pygraphviz_layout(composite_graph,
prog="neato",
args='-Gstart=5')
except ImportError:
logger.warning(
'could not import pygraphviz. Falling back to force directed')
pos = nx.fruchterman_reingold_layout(composite_graph, seed=5)
if not pos:
return None, None
nx_labels = {} # from k to label
min_x = min(x for x, y in pos.values())
min_y = min(y for x, y in pos.values())
att_rows = []
for k, (labels, genes_lists) in sorted(att.items()):
if k not in pos:
logger.warning('node not in graph: %s', k)
continue
nx_labels[k] = label = ' '.join(labels)
types = ','.join(['gene'] * len(labels))
gene_list = ',/,'.join(','.join(gene_list)
for gene_list in genes_lists)
x, y = pos[k]
att_rows.append((
k, # 1. ID
label, # 2. label
int(100 * (x - min_x)), # 3. X
int(100 * (y - min_y)), # 4. Y
'white', # 5. color
'rectangle', # 6. shape
types, # 7.
0.5, # 8. label.cex
'black', # 9. label.color
46, # 10. width
17, # 11. height
gene_list, # 12. gene list
))
att_df = pd.DataFrame(att_rows,
columns=[
'ID', 'label', 'X', 'Y', 'color', 'shape',
'type', 'label.cex', 'label.color', 'width',
'height', 'genesList'
])
if draw_directory is not None:
try:
import matplotlib.pyplot as plt
except ImportError:
logger.warning(
'could not draw graph because matplotlib is not installed')
else:
plt.figure(figsize=(20, 20))
nx.draw_networkx(composite_graph, pos, labels=nx_labels)
plt.axis('off')
plt.savefig(
os.path.join(draw_directory, '{}.png'.format(graph.name)))
return att_df, sif_df
import networkx as nx
from networkx.drawing.nx_agraph import write_dot, graphviz_layout, pygraphviz_layout
import matplotlib.pyplot as plt
G = nx.DiGraph()
G.add_node("ROOT")
for i in range(5):
G.add_node("Child_%i" % i)
G.add_node("Grandchild_%i" % i)
G.add_node("Greatgrandchild_%i" % i)
G.add_edge("ROOT", "Child_%i" % i)
G.add_edge("Child_%i" % i, "Grandchild_%i" % i)
G.add_edge("Grandchild_%i" % i, "Greatgrandchild_%i" % i)
# write dot file to use with graphviz
# run "dot -Tpng test.dot >test.png"
write_dot(G, 'test.dot')
# same layout using matplotlib with no labels
plt.title('draw_networkx')
pos = pygraphviz_layout(G, prog='dot')
print(pos)
nx.draw(G, pos, with_labels=False, arrows=True)
plt.savefig('nx_test.png')
def plot_examples(self, atom_number, cutoff, number, feed_dict={}):
import networkx as nx
import matplotlib.pyplot as plt
from networkx.drawing.nx_agraph import pygraphviz_layout
def fit(g, n):
if 'mask' not in g.nodes[n]:
return 0
if g.nodes[n]['mask'] > 0.1:
return abs(g.nodes[n]['peak'] - g.nodes[n]['label'])
return 0
def color_fit(g, n, cmap, vmin, vmax):
f = fit(g, n)
if f == 0:
return (1,1,1,0)
else:
return cmap((f - vmin) / vmax)
mols = []
vmax = 0
candidates = self.to_networkx(number=number * 25)
for g in candidates:
for n in g.nodes():
error = fit(g, n)
if error > cutoff:
if error > vmax:
vmax = error
mols.append(g)
break
# trim to size
mols = mols[:number]
grid = int(np.sqrt(len(mols)))
fig, axs = plt.subplots(grid, grid, figsize=(32, 32))
viridis = plt.get_cmap('viridis', 100)
for i in range(grid):
for j in range(grid):
ax = axs[i,j]
g = mols[i * grid + j]
r = []
if atom_number - 1 in g.nodes:
g.remove_node(atom_number - 1)
c = [color_fit(g,n,viridis, 0, vmax) for n in g.nodes]
# now remove all non single-bond edges
remove = []
for e in g.edges(data=True):
if not e[2]['bonded']:
if 'mask' not in g.nodes[e[1]] or 'mask' not in g.nodes[e[0]]:
#TODO how is this happening?
remove.append(e)
elif g.nodes[e[0]]['mask'] < .1 and g.nodes[e[1]]['mask'] < 0.1:
remove.append(e)
g.remove_edges_from(remove)
pos = pygraphviz_layout(g, prog='sfdp', args='-Gmaxiter=150 -Gnodesep=100 -Nshape=circle')
edge_colors = [(0,0,0) if d['bonded'] else (0.8, 0.8, 0.8) for e1,e2,d in g.edges(data=True)]
#pos = nx.layout.spring_layout(g, iterations=150, k=0.2)
nx.draw(g,
pos,
node_size=60,
fontsize=5,
node_color=c,
vmin=0,
vmax=vmax,
labels={n: g.nodes[n]['name'] if'mask' in g.nodes[n] and g.nodes[n]['mask'] < 0.1 else '' for n in g.nodes},
with_labels=True,
edge_color=edge_colors,
ax=ax
)
ax.axis('on')
ax.set_yticklabels([])
ax.set_xticklabels([])
ax.get_xaxis().set_ticks([])
ax.get_yaxis().set_ticks([])
ax.set_title(g.graph['class_label'] + ':' + ','.join([str(i) for i in g.graph['record_index']]))
cm = plt.cm.ScalarMappable(cmap=viridis, norm=plt.Normalize(vmin = 0, vmax=vmax))
cb = plt.colorbar(cm, shrink=0.8)
cb.ax.get_yaxis().labelpad = 15
cb.ax.tick_params(labelsize=16)
cb.ax.set_ylabel('Prediction Error', rotation=270, fontsize=16)
plt.savefig(self.model_path + '/plots/' + 'examples-{:.2f}.jpg'.format(cutoff), dpi=300, transparent=True)
plt.close()
def slimpass(bn: TWBayesianNetwork,
budget: int = BUDGET,
timeout: int = TIMEOUT,
history: Counter = None,
width_bound: int = None,
debug=False):
td = bn.td
if USING_COMPLEXITY_WIDTH:
final_width_bound = weight_from_domain_size(width_bound)
else:
final_width_bound = width_bound
selected, seen = find_subtree(td, budget, history, debug=False)
history.update(selected)
prep_tuple = prepare_subtree(bn, selected, seen, debug)
if prep_tuple is None: return
forced_arcs, forced_cliques, data, pset_acyc = prep_tuple
# if debug:
# print("filtered data:-")
# pprint(data)
old_score = bn.compute_score(seen)
max_score = compute_max_score(data, bn)
if RELAXED_PARENTS:
# too strict
# assert max_score + EPSILON >= old_score, "max score less than old score"
assert round(max_score + EPSILON, 4) >= round(
old_score, 4), "max score less than old score"
if max_score < old_score:
print("#### max score smaller than old score modulo epsilon")
cur_offset = sum(bn.offsets[node] for node in seen)
if debug:
print(
f"potential max: {(max_score - cur_offset)/bn.best_norm_score:.5f}",
end="")
if (max_score - cur_offset) / bn.best_norm_score <= LAZY_THRESHOLD:
if debug: print(" skipping because lazy threshold not met")
SOLUTION.skipped += 1
return
pos = dict() # placeholder layout
if not CLUSTER and debug:
pos = pygraphviz_layout(bn.dag, prog='dot')
nx.draw(bn.dag, pos, with_labels=True)
plt.suptitle("entire dag")
plt.show()
nx.draw(bn.dag.subgraph(seen), pos, with_labels=True)
plt.suptitle("subdag before improvement")
plt.show()
if debug:
print("old parents:-")
pprint({node: par for node, par in bn.parents.items() if node in seen})
domain_sizes = DOMAIN_SIZES if USING_COMPLEXITY_WIDTH else None
try:
replbn = solve_bn(data, final_width_bound, bn.input_file, forced_arcs,
forced_cliques, pset_acyc, timeout, domain_sizes,
debug)
except NoSolutionException as err:
SOLUTION.nosolution += 1
print(f"no solution found by maxsat, skipping (reason: {err})")
return
new_score = replbn.compute_score()
if not CLUSTER and debug:
nx.draw(replbn.dag, pos, with_labels=True)
plt.suptitle("replacement subdag")
plt.show()
if debug:
print("new parents:-")
pprint(replbn.parents)
if debug: print(f"score change: {old_score:.3f} -> {new_score:.3f}")
if USE_COMPLEXITY_WIDTH:
old_cw = compute_complexity_width(td, DOMAIN_SIZES, include=selected)
new_cw = compute_complexity_width(replbn.td, DOMAIN_SIZES)
old_acw = compute_complexity_width(td,
DOMAIN_SIZES,
include=selected,
approx=True)
new_acw = compute_complexity_width(replbn.td,
DOMAIN_SIZES,
approx=True)
# print(f"old: {old_cw}|{old_acw:.3f}\tnew: {new_cw}|{new_acw:.3f}")
print(f"msss of local part: {old_cw} -> {new_cw}")
# replacement criterion
if USING_COMPLEXITY_WIDTH and old_cw > width_bound:
if new_cw > width_bound:
return False
elif USING_COMPLEXITY_WIDTH and new_score == old_score and new_cw > old_cw:
return False
elif new_score < old_score: # in case not using cw, then this is the only check
return False
print(f"score change: {old_score:.3f} -> {new_score:.3f}, replacing ...")
td.replace(selected, forced_cliques, replbn.td)
# update bn with new bn
bn.replace(replbn)
if __debug__: bn.verify(verify_treewidth=not USING_COMPLEXITY_WIDTH)
return True
networks = ['CRM'] # IDs of networks we are looking at
layoutprog = "neato" # sfdp gives more stretched out layout
SCALE = 10
# CODE
for network in networks:
infile = "{}/{}_network.gexf".format(infolder, network)
# Read in
G = nx.read_gexf(infile) # Name lost?
H = sorted(nx.connected_component_subgraphs(G), key=len, reverse=True)[0] # get giant component
# Calculate node positions and centralities
node_positions = pygraphviz_layout(H, prog=layoutprog) # See https://networkx.github.io/documentation/latest/reference/drawing.html#layout
node_betweenness = nx.betweenness_centrality(H) # See https://networkx.github.io/documentation/latest/reference/algorithms.centrality.html
i = 1
for node, data in H.nodes_iter(data=True): # add IDs and scale
data["id"] = i
i += 1
data["x"], data["y"] = tuple(x*SCALE for x in node_positions[node])
data["betweenness"] = node_betweenness[node]
# GRAPH VISUALIZATION
# Generate JS
nodes = {}
# nodes for 'function'; groupnumber for groupvalue
nodes['f'] = ['{id:%d,label:"%s",group:"%s",title:"%s<br></br>%s",x:%s,y:%s,value:0.5}'
% (data["id"], data['label'], data["group"], data['label'], data["meta"], data["x"], data["y"])
for node, data in H.nodes(data=True)]
def draw_graph(self, graph):
plt.title('draw_networkx')
pos=pygraphviz_layout(graph, prog='dot', args='-Gnodesep=1')
nx.draw(graph, pos, node_size=30, with_labels=False, arrows=True)
plt.savefig('nx_test.png')
plt.close()