def to_pyvis(graph, layout=True):
"""
This method takes an exisitng Networkx graph and translates
it to a PyVis graph format that can be accepted by the VisJs
API in the Jinja2 template.
Parameters
----------
graph : nx.DiGraph
NetworkX directed graph.
layout : bool
Use hierarchical layout if this is set.
Returns
-------
net : Network
PyVis Network
"""
def add_node(node_id):
attr = nodes[node_id]
net.add_node(node_id, label=attr['label'], level=attr['level'], color=attr.get('color', None),
title=attr['title'])
edges = graph.edges.data()
nodes = graph.nodes
net = Network(height="960px", width="1280px", directed=True, layout=layout)
for v, u, edge_attr in edges:
add_node(v)
add_node(u)
net.add_edge(v, u, title=edge_attr['label'], color=edge_attr['color'])
return net
def wrapper(jsonGraph, path):
g = func(jsonGraph,path)
colors = dict(mcolors.BASE_COLORS, **mcolors.CSS4_COLORS)
G= Network(height="800px", width="70%", directed=True)
data=[]
for u,e,v in g[1]:
data.append(e)
label_encoder = LabelEncoder()
integer_encoded = np.array(label_encoder.fit_transform(data), dtype='float')
i=0
for src,e,dst in g[1]:
src_cname_idx = str(src).count('/') if str(src).count('/') < len(cnames) else (len(cnames) - 1)
src_size_idx = str(src).count('/') if str(src).count('/') < len(sizes) else (len(sizes) - 1)
dst_cname_idx = str(dst).count('/') if str(dst).count('/') < len(cnames) else (len(cnames) - 1)
dst_size_idx = str(dst).count('/') if str(dst).count('/') < len(sizes) else (len(sizes) - 1)
G.add_node(src, title=src, physics=True,color=cnames[src_cname_idx], size=sizes[src_size_idx], shape="dot")
G.add_node(dst, title=dst, physics=True,color=cnames[dst_cname_idx], size=sizes[dst_size_idx], shape="dot")
G.add_edge(src,dst,width=0.5, title=data[i],physics=True)
i+=1
G.hrepulsion(node_distance=120,
central_gravity=0.0,
spring_length=100,
spring_strength=0.01,
damping=0.09)
G.show_buttons(filter_=['physics'])
G.show("test.html")
# for s,p,o in g[1]:
# print((s,p,o))
return g
def to_interactive_html(self, destination: str):
from pyvis.network import Network # type: ignore
G = Network(height='100%',
width='100%',
directed=True,
bgcolor='#000000')
G.toggle_stabilization(False)
all_nodes: Set[Node] = set()
nodes_to_explore: Set[Node] = set([self])
while len(nodes_to_explore) > 0:
all_nodes.update(nodes_to_explore)
new_nodes_to_explore: Set[Node] = set()
for node_to_explore in nodes_to_explore:
connected_nodes = node_to_explore.query.through_edge().results
connected_nodes = cast(Set[Node], connected_nodes)
new_nodes_to_explore.update([
node for node in connected_nodes if node not in all_nodes
])
nodes_to_explore = new_nodes_to_explore
for node in all_nodes:
G.add_node(node.graph_id, label=str(node))
for node in all_nodes:
for out in node.outbound:
G.add_edge(node.graph_id, out.destination.graph_id)
# links.append((node, out.destination, {'label': out.label}))
G.show(destination)
def network_visualization(path='./socnetvis.html', alphabet=False):
weights = {'best': 4, 'good': 2, 'friend': 1, 'acquaintance': 0.5}
net = Network('100%', '100%', bgcolor='#222', font_color='white')
net.barnes_hut()
for name, node in nodes.items():
for connection_type in node['connections']:
for partner in node['connections'][connection_type]:
net.add_node(name, name, title=name)
net.add_node(partner, partner, title=partner)
net.add_edge(name, partner, value=weights[connection_type])
for net_node in net.nodes:
node = nodes[net_node['id']]
net_node['value'] = len(net.get_adj_list()[net_node['id']])
net_node['title'] += f"<br>{net_node['value']} Connections<br>"
if node['notes']:
net_node['title'] += f"<i>{node['notes']}</i><br>"
for connection_type in node['connections']:
if node['connections'][connection_type]:
connections = node['connections'][connection_type]
net_node['title'] += f"<br>{connection_type.capitalize()} " \
f"({len(connections)})<br>  "
net_node['title'] += "<br>  ".join(
sorted(connections) if alphabet else connections) + "<br>"
if not os.path.isdir(os.path.dirname(path)):
os.makedirs(os.path.dirname(path))
net.show(path)
def graph_print():
dist = loadCompleteDistro()
matrix = numpy.zeros((len(dist), len(dist)))
i = 0
labels = {}
net = Network()
k=0
caster = {"nld": "Niderlandzki", "gle": "Irlandzki", "spa": "Hiszpański", "fra": "Francuski", "eng": "Angielski", "slk": "Słowacki", "fin": "Fiński", "est": "Estoński", "lit": "Litewski", "hrv": "Chorwacki", "por": "Portugalski", "swe": "Szwedzki", "ron": "Romański", "dan": "Duński", "slv": "Słoweński", "bul": "Bułgarski", "ita": "Włoski", "ell": "Grecki", "mlt": "Maltański", "lav": "Łotewski", "ces": "Czeski", "pol": "Polski", "deu": "Niemiecki", "hun": "Węgierski"}
for lang1 in dist.keys():
print(lang1)
net.add_node(k + 1, label=f"{caster[lang1]}")
k+=1
xD = []
for lang1 in dist.keys():
labels[i] = lang1
j = 0
for lang2 in dist.keys():
if lang1 != lang2:
xD.append([i+1, j+1,round(KullbackLeibnerIteration(dist[lang1].alain(dist[lang2]), dist[lang2].alain(dist[lang1])),2)])
else:
pass
j += 1
i += 1
#G = nx.from_numpy_matrix(matrix)
#H = nx.relabel_nodes(G, labels)
#vg = []
#for u in H.edges.data():
# vg.append(u[2]["weight"])
#
xD.sort(key=lambda x: x[2])
xDD = xD[:40]
for x in xDD:
print(x[2])
net.add_edge(x[0],x[1],value=1.0/x[2], label=str(x[2]))
#
#Z = copy.deepcopy(H)
#for u in Z.edges.data():
# if u[2]["weight"] > median:
# H.remove_edge(u[0], u[1])
#
#pos = nx.spring_layout(H,k=1, iterations=20)
#plt.figure(3, figsize=(10, 10))
#labels = nx.get_edge_attributes(H, 'weight')
#nx.draw_networkx(H,pos=pos, with_labels=True,node_size=500)
#nx.draw_networkx_edge_labels(H, pos, edge_labels=labels)
#plt.show()
net.save_graph("my_graph.html")
net.toggle_physics(True)
net.show_buttons(filter_=['nodes', 'edges', 'physics'])
net.show('mygraph.html')
class transaction_graph:
def __init__(self):
self.graph = Network(height="750px", width="100%", directed=True)
with open('layouts\\transaction_graph_layout.json') as f:
self.options = json.load(f)
def show_graph(self):
dirOutput = "output"
if not os.path.exists(dirOutput):
os.makedirs("output")
self.graph.show("output\\transaction_gragh.html")
def add_transaction(self, input, output, in_time, out_time, amount):
input_edge = zip(input, in_time, output, out_time, amount)
for i in input_edge:
input = i[0]
label = i[0]
time_in = i[1]
output = i[2]
time_out = i[3]
weight = i[4]
self.graph.add_node(input, level=time_in, shape="square")
self.graph.add_node(output, level=time_out, shape="square")
self.graph.add_edge(input, output, value=weight, title=weight)
self.graph.options = self.options
def visualize(networkx_graph, name):
if '.html' in name:
pyvis_graph = Network(height=800, width=800, notebook=True)
for node, node_attrs in networkx_graph.nodes(data=True):
pyvis_graph.add_node(node, **node_attrs)
# for each edge and its attributes in the networkx graph
for source, target, edge_attrs in networkx_graph.edges(data=True):
# if value/width not specified directly, and weight is specified, set 'value' to 'weight'
if not 'value' in edge_attrs and not 'width' in edge_attrs and 'weight' in edge_attrs:
# place at key 'value' the weight of the edge
edge_attrs['value'] = edge_attrs['weight']
# add the edge
pyvis_graph.add_edge(source, target, **edge_attrs)
return pyvis_graph.show('docs/' + name)
elif '.svg' in name:
# pos = nx.spring_layout(networkx_graph,k=0.25)
options = {
"node_color": "blue",
"node_size": 20,
"line_color": "grey",
"linewidths": 1,
"width": 1,
}
nx.draw(networkx_graph, **options)
plt.savefig(f"docs/{name}")
def network_pyvis(self, df):
G = nx.from_pandas_edgelist(df, edge_attr=True)
net = Network(height="500px", width="100%", heading='')
sources = df['source']
targets = df['target']
weights = df['weight']
edge_data = zip(sources, targets, weights)
for e in edge_data:
src = e[0]
dst = e[1]
w = e[2]
net.add_node(src, src, title=src)
net.add_node(dst, dst, title=dst)
net.add_edge(src, dst, value=w)
neighbor_map = net.get_adj_list()
net.from_nx(G)
net.write_html('tweets/temp.html')
return net.html
def plotResult(file_in, file_out):
got_net = Network(height="100%",
width="100%",
bgcolor="white",
font_color="black")
got_net.barnes_hut()
got_data = pd.read_csv(file_in)
sources = got_data['From']
targets = got_data['To']
weights = got_data['Weight']
x_array = got_data['x']
y_array = got_data['y']
highlight = got_data['Highlight']
edge_data = zip(sources, targets, weights, x_array, y_array, highlight)
for e in edge_data:
src = e[0]
dst = e[1]
w = e[2]
x_array = e[3]
y_array = e[4]
h = e[5]
v_color_dst = "#ADFF2F" #Green color
image_url = 'cat.png'
v_shape = 'dot'
if (dst in ['central_concentrator'] or h == 1):
image_url = 'cat.png'
v_shape = 'circle'
got_net.add_node(src,
shape=v_shape,
title=src,
x=x_array,
y=y_array,
color="#ADFF2F") #Green color
got_net.add_node(dst,
shape=v_shape,
title=dst,
x=x_array,
y=y_array,
color=v_color_dst)
got_net.add_edge(src, dst, value=h)
neighbor_map = got_net.get_adj_list()
# add neighbor data to node hover data
for node in got_net.nodes:
node["title"] += " Neighbors:<br>" + "<br>".join(
neighbor_map[node["id"]])
node["value"] = len(neighbor_map[node["id"]])
got_net.set_options(
'var options = { "edges": { "arrows": { "middle": { "enabled": true } }, "color": { "inherit": "false"}, "smooth": false},"physics": {"enabled": true, "forceAtlas2Based":{ "gravitationalConstant": -500, "springLength": 100, "avoidOverlap": 1}, "minVelocity": 0.75, "solver": "forceAtlas2Based"}}'
)
got_net.show(file_out)
def getCourseText():
"""
Visualize courses and their assigned texts.
"""
coursesAndTexts = g.query("""
select distinct ?courseName ?textTitle ?authorLast where {
?a a ccso:Course .
?a ccso:csName ?courseName .
?a ccso:hasLM ?t .
?t res:resource ?doc .
?doc dcterms:title ?textTitle .
?doc dcterms:creator ?author .
?author foaf:surname ?authorLast .
} limit 50""")
for line in coursesAndTexts:
print(line)
net = Network(height='750px', width='100%')
for courseName, textTitle, authorLast in coursesAndTexts:
net.add_node(courseName, shape='square', title=str(courseName))
net.add_node(textTitle,
shape='circle',
label=str(authorLast),
title=str(textTitle))
net.add_edge(courseName, textTitle, title="hasLM")
net.save_graph('../website/graph-viz.html')
def build_pyvis(filename):
header = metadata_header(filename)
net = Network("95%", "100%", heading=header)
net.show_buttons()
nodes, edges = triplet(filename)
node_weight = count_node_weight(edges)
for node in nodes:
group = node["labels"] if node["labels"] else ""
net.add_node(
node["alias"],
label=node["name"],
group=group,
size=((sqrt(node_weight[node["alias"]]) + 1) * 5),
)
for edge in edges:
net.add_node(edge["subject"], color="blue")
net.add_node(edge["object"], color="blue")
net.add_edge(edge["subject"], edge["object"], title=edge["predicate"])
net.barnes_hut(
gravity=-4000,
central_gravity=0.3,
spring_strength=0.001,
damping=0.09,
overlap=1,
)
net.show("index.html")
def getUniCourseGraph():
"""
Get university-course graph.
"""
results = g.query("""
select distinct ?courseID ?courseName ?instructorFN ?instructorGN ?university where {
?courseID a ccso:Course .
?courseID ccso:csName ?courseName .
?courseID ccso:hasInstructor ?inst .
?inst foaf:familyName ?instructorFN .
?inst foaf:givenName ?instructorGN .
?courseID ccso:offeredBy ?dept .
?dept ccso:belongsTo ?uni .
?uni ccso:legalName ?university .
}""")
visGraph = Network(height='750px',
width='100%') # PyVis-Network, for visualization.
nxGraph = nx.Graph() # NetworkX, for analyses
for courseID, courseName, instLast, instFirst, uni in results:
instName = f"{instFirst} {instLast}"
nxGraph.add_node(uni)
visGraph.add_node(uni, shape='circle', title=uni, mass=2)
nxGraph.add_node(courseID)
visGraph.add_node(courseID, shape='box', label=courseName)
visGraph.add_edge(uni, courseID)
nxGraph.add_edge(uni, courseID)
return nxGraph, visGraph
def generate_graph(arbre):
got_net = Network(height="100%",
width="100%",
bgcolor="#222222",
font_color="white")
dico_couleur = {}
for streamer in arbre.streamers:
got_net.add_node(streamer.name,
value=streamer.poids,
shape='image',
image=streamer.photo_profil,
size=100)
dico_couleur[streamer.name] = streamer.couleur
for depart, arrivee in arbre.groupes_migrants:
for viewer in arbre.groupes_migrants[depart, arrivee]:
got_net.add_node(viewer, value=1, color=dico_couleur[depart])
got_net.add_edge(viewer, depart, color=dico_couleur[depart])
got_net.add_edge(viewer, arrivee, color=dico_couleur[arrivee])
got_net.show_buttons()
got_net.set_edge_smooth(smooth_type='dynamic')
got_net.force_atlas_2based(gravity=-200,
central_gravity=0.01,
spring_length=1,
spring_strength=0.08,
damping=0.4,
overlap=0)
got_net.save_graph("./graphs_v1/" + 'streamgame_v1_42' + ".html")
return
def api_docs_network():
ee = get_enriched_endpoints()
endpoints = [e['endpoint'] for e in ee]
similarity_matrix = similarity_network([e['document'] for e in ee], weighted=True, enr_endpoints=ee)
similarity_threshold = 0.7
colors = get_different_colors(305)
added_nodes = []
wordnet_network = nx.Graph()
vis_network = Network(height="100%", width="70%")
for iy, y in enumerate(similarity_matrix):
for ix, x in enumerate(y):
if x > similarity_threshold and ix != iy:
y_name = endpoints[iy]['path']
x_name = endpoints[ix]['path']
if y_name not in added_nodes:
vis_network.add_node(y_name)
# vis_network.add_node(y_name,
# color="#FF0000" if len(get_services_from_table(y_name)) > 0 else "#DDDDDD")
added_nodes.append(y_name)
if x_name not in added_nodes:
vis_network.add_node(x_name)
# vis_network.add_node(x_name,
# color="#FF0000" if len(get_services_from_table(y_name)) > 0 else "#DDDDDD")
added_nodes.append(x_name)
# norm_weight = (x - similarity_threshold) / (1 - similarity_threshold)
vis_network.add_edge(y_name, x_name)
wordnet_network.add_edge(y_name, x_name, weight=x)
nx.write_gexf(wordnet_network, "network_outputs/api_wordnet.gexf")
nx.draw_networkx(wordnet_network, node_size=3, with_labels=False)
plt.show()
vis_network.show_buttons(filter_=['physics'])
vis_network.show("network_outputs/api_wordnet.html")
def evaluate_match_based(video_space, estimator, plot=True, thr=0.4):
estimator.fit(video_space)
distances, indexes = estimator.kneighbors(video_space, n_neighbors=20)
if plot == True:
plt.hist(distances[:, 1::].ravel(), bins=100)
results, results_distances = filter_results(distances, indexes, thr)
net = Network(notebook=True, height='1000px', width='1000px')
net.barnes_hut()
for i, l in enumerate(labels):
net.add_node(str(i), label=str(l))
for i, d in enumerate(results):
for j, m in enumerate(d):
if j != 0:
net.add_edge(str(i),
str(m),
weight=str(results_distances[i][j]))
net.show_buttons(filter_=['physics'])
net.show('mygraph.html')
return net
def plot_bacteria_intraction_network(bacteria, node_list, node_size_list, edge_list, color_list, G_name, folder,
color_by_tax_level=2, directed_G=True, control_color_and_shape=True):
# create the results folder
if not os.path.exists(folder):
os.mkdir(folder)
nodes_colors, nodes_shapes, group_list, tax_to_color_and_shape_map = \
get_nodes_colors_by_bacteria_tax_level(bacteria, G_name, taxnomy_level=color_by_tax_level, folder=folder)
bact_short_names = [shorten_single_bact_name(b) for b in bacteria]
nodes_with_edges = np.unique(np.array(edge_list).flatten()).tolist()
net = Network(height="750px", width="100%", bgcolor="#FFFFFF", font_color="black", directed=directed_G)
#net.barnes_hut(gravity=-120000)
net.force_atlas_2based()
# for the nodes: you can use either only the group option the automatically colors the group in different colors
# shaped like dots - no control, or use color and shape to make it you own, in this case group is irrelevant
for i, node in enumerate(node_list):
if node in nodes_with_edges:
if control_color_and_shape:
net.add_node(node, label=bact_short_names[i], color=nodes_colors[i], value=node_size_list[i],
shape=nodes_shapes[i], group=group_list[i])
else:
net.add_node(node, label=bact_short_names[i], value=node_size_list[i],
group=group_list[i])
# for the edges, the colors are what you decide and send
for i, (u, v) in enumerate(edge_list):
net.add_edge(u, v, color=color_list[i])
net.save_graph(os.path.join(folder, G_name + ".html"))
def pyvis(height):
# Load Pyvis network
got_net = Network(height="750px",
width="100%",
bgcolor="#222222",
font_color="white")
got_net.barnes_hut()
got_data = pd.read_csv(
"https://www.macalester.edu/~abeverid/data/stormofswords.csv")
sources = got_data['Source']
targets = got_data['Target']
weights = got_data['Weight']
edge_data = zip(sources, targets, weights)
for e in edge_data:
src = e[0]
dst = e[1]
w = e[2]
got_net.add_node(src, src, title=src)
got_net.add_node(dst, dst, title=dst)
got_net.add_edge(src, dst, value=w)
neighbor_map = got_net.get_adj_list()
for node in got_net.nodes:
node["title"] += " Neighbors:<br>" + "<br>".join(
neighbor_map[node["id"]])
node["value"] = len(neighbor_map[node["id"]])
got_net.write_html("gameofthrones.html")
return got_net.html, height, "Pyvis Network"
class show_path:
def __init__(self):
self.graph = Network(height="750px", width="100%", directed=True)
with open('layouts\path_layout.json') as f:
self.composite_options = json.load(f)
def show_graph(self):
dirOutput = "output"
if not os.path.exists(dirOutput):
os.makedirs("output")
self.graph.show("output\path_graph.html")
def add_path(self, input, amount):
input_edge = zip(input[0:len(input) - 1], input[1:len(input)], amount)
for i in input_edge:
input = i[0]
output = i[1]
weight = i[2]
self.graph.add_node(input)
self.graph.add_node(output)
self.graph.add_edge(input, output, value=weight, title=weight)
self.graph.options = self.composite_options
def show(self):
self.show_graph()
def kyoki_word_network():
got_net = Network(height="1000px",
width="95%",
bgcolor="#FFFFFF",
font_color="black",
notebook=True)
# set the physics layout of the network
#got_net.barnes_hut()
got_net.force_atlas_2based()
got_data = pd.read_csv("kyoki.csv")[:150]
sources = got_data['first'] #count
targets = got_data['second'] #first
weights = got_data['count'] #second
edge_data = zip(sources, targets, weights)
for e in edge_data:
src = e[0]
dst = e[1]
w = e[2]
got_net.add_node(src, src, title=src)
got_net.add_node(dst, dst, title=dst)
got_net.add_edge(src, dst, value=w)
neighbor_map = got_net.get_adj_list()
#add neighbor data to node hover data
for node in got_net.nodes:
node["title"] += " Neighbors:<br>" + "<br>".join(
neighbor_map[node["id"]])
node["value"] = len(neighbor_map[node["id"]])
got_net.show_buttons(filter_=['physics'])
return got_net
def createNetwork(in_dic, showNodesPanel_bol, showPhysicsPanel_bol):
"""Function to take a dic and to build a network from it. Key = pmid, value = [refs]. We can selected whether we want panel to edit nodes or gravity
in_dic must have format;
[+] pmid_dic = {pmid_int : [[ref1_str, ..., refn_str], title_str]}
[+] in_dic :{19102772: [[12764516, 15825143, 15702043], 'Identification of a novel picornavirus related to cosaviruses in a child with acute diarrhea'], 31622334: [[20536486, 17627978], 'Use of personalised risk-based screening schedules to optimise workload and sojourn time in screening programmes for diabetic retinopathy: A retrospective cohort study']}.
"""
#get the network ready
G = Network(height="100%",
width="95%",
bgcolor="#222222",
font_color="white")
#G.barnes_hut()
# add the reference nodes
for i in in_dic:
# add a link to the article on pubmed
myTitle_str = in_dic[i][1]
# addToMyTitle_str = '<a href="https://pubmed.ncbi.nlm.nih.gov/{}" target="_blank"> Link:{}'.format(i,i)
addToMyTitle_str = '<a href="https://pubmed.ncbi.nlm.nih.gov/{}" target="_blank">'.format(
i)
myTitle_str = addToMyTitle_str + myTitle_str
#st.write("i = {} and list of refs = {}, title = {}".format(i, in_dic[i][0], myTitle_str))
# main node
G.add_node(str(i), color="#dd4b39", value=1,
title=myTitle_str) #, mass = 10)# [1] = title
# reference nodes
# are there any refs for the node?
if len(in_dic[i][0]) != 0:
for j in in_dic[i][0]: # [0] = ref nodes
#st.write("REF Node j :{}".format(j))
refNode_str = str(j) # add main node
#st.write("pmid = <{}>, adding ref node j <<{}>>".format(i, refNode_str))
# add the ref node; no titles to give so we use the pubmed link instead.
myTitle = '<a href="https://pubmed.ncbi.nlm.nih.gov/{}" target="_blank"> Link:{}'.format(
refNode_str, refNode_str)
G.add_node(refNode_str, title=myTitle)
# draw edge between main node and ref node
G.add_edge(str(i), refNode_str, value=1)
else:
# st.write("pmid = <{}> has no references. :-(".format(i))
pass
if showNodesPanel_bol == True:
G.show_buttons(filter_=['nodes']) #shown below graph in browser
# G.show_buttons(filter_=['physics']) #shown below graph in browser
if showPhysicsPanel_bol == True:
G.show_buttons(filter_=['physics']) #shown below graph in browser
phc.checkDataDir(OUTDATADIR)
plotName_str = OUTDATADIR + "pmidPlot.html"
# plotName_str = "/tmp/pmidPlot.html"
showMyPlot(G, plotName_str) #push out the plot to browser
class NetDisplay:
def __init__(self, net, LinGen, name):
self.net = net
self.LinGen = LinGen
self.Grafo = Network(height="600px", width="1000px")
self.name = name
self.Grafo.toggle_physics(False)
self.Grafo.inherit_edge_colors_from(False)
def nodesPlot(self):
self.CalcNeuronsYpositions()
for layer in self.net:
neurons = layer.ReturnNeurons()
y_positions = layer.NeuronYPosition
for neuron, y_pos in zip(neurons, y_positions):
self.Grafo.add_node(
neuron, x=layer.number * 100, y=y_pos * 100)
i = 0
for con in self.LinGen:
if con.enable:
if con.weight >= 0:
color = 'blue'
else:
color = 'red'
if con.recurrent:
dashes = 'true'
else:
dashes = 'false'
try:
self.Grafo.add_edge(
con.input, con.output, value=abs(con.weight))
self.Grafo.edges[i].update(
{'color': color, 'arrows': 'to', 'arrowStrikethrough': 'false',
'title': 'IN: ' + str(con.innovation_number), 'dashes': dashes, 'shadow': dashes})
i += 1
except:
pass
self.Grafo.show_buttons()
self.Grafo.set_edge_smooth('dynamic')
self.Grafo.show(self.name + ".html")
def CalcNeuronsYpositions(self):
for layer in self.net:
neuronsYposition = []
size = len(layer.ReturnNeurons())
if size % 2 == 0:
for i in range(0, size // 2):
neuronsYposition += [i + 0.5, -i - 0.5]
else:
neuronsYposition = [0]
for i in range(1, size // 2 + 1):
neuronsYposition += [i, -i]
layer.NeuronYPosition = neuronsYposition
def drawRscRscGraph_advanced(self, RscRscMatrix, weight_threshold, directed, encryption):
rows, cols = np.where(RscRscMatrix > weight_threshold)
weights = list();
for x in range(len(rows)):
weights.append(RscRscMatrix[rows[x]][cols[x]])
#got_net = Network(height="750px", width="100%", bgcolor="white", font_color="#3de975", directed=directed)
got_net = Network(height="750px", width="100%", bgcolor="white", font_color="black", directed=directed)
##f57b2b
# set the physics layout of the network
got_net.barnes_hut()
edge_data = zip(rows, cols, weights)
for e in edge_data:
src = self.resourceList[e[0]] # convert ids to labels
dst = self.resourceList[e[1]]
w = e[2]
if(encryption):
src = Utilities.AES_ECB_Encrypt(self,src.encode('utf-8'))
dst = Utilities.AES_ECB_Encrypt(self,dst.encode('utf-8'))
# I have to add some options here, there is no parameter
highlight = {'border': "#3de975", 'background': "#41e9df"}
#color = {'border': "#000000", 'background': "#123456"}
got_net.add_node(src, src, title=src, labelHighlightBold=True, color={'highlight': highlight})
got_net.add_node(dst, dst, title=dst , labelHighlightBold=True, color={'highlight': highlight})
got_net.add_edge(src, dst, value=w, title=w)
neighbor_map = got_net.get_adj_list()
dict = got_net.get_edges()
self.getResourceList()
# add neighbor data to node hover data
for node in got_net.nodes:
counter = 0
if(directed):
node["title"] = "<h3>" + node["title"] + " Output Links: </h3>"
else:
node["title"] = "<h3>" + node["title"] + " Links: </h3>"
for neighbor in neighbor_map[node["id"]]:
if(counter % 10 == 0):
node["title"] += "<br>::: " + neighbor
else:
node["title"] += " ::: " + neighbor
node["value"] = len(neighbor_map[node["id"]])
counter += 1
got_net.show_buttons(filter_=['nodes', 'edges', 'physics'])
got_net.show_buttons(filter_=['physics'])
got_net.show("PMSocial.html")
def drawActivityResourceGraph_advanced(self, ActivityRscMatrix, weight_threshold, directed, splitted):
rows, cols = np.where(ActivityRscMatrix > weight_threshold)
weights = list();
for x in range(len(rows)):
weights.append(ActivityRscMatrix[rows[x]][cols[x]])
got_net = Network(height="750px", width="100%", bgcolor="black", font_color="#f57b2b", directed= directed)
# set the physics layout of the network
got_net.barnes_hut()
edge_data = zip(rows, cols, weights)
counter = 1
for e in edge_data:
src = self.activityList[e[0]] # convert ids to labels
dst = self.resourceList[e[1]]
w = e[2]
# I have to add some options here, there is no parameter
highlight = {'border': "#3de975", 'background': "#41e9df"}
if(splitted):
got_net.add_node(src, src, title=src, labelHighlightBold=True, color={'highlight': highlight},shape='square')
got_net.add_node(dst+ "__" +str(counter) , dst , title=dst , labelHighlightBold=True, color={'border': "#dd4b39", 'background': "#dd4b39", 'highlight': highlight})
got_net.add_edge(src, dst+ "__" +str(counter), value=w, title=w)
counter +=1
else:
got_net.add_node(src, src, title=src, labelHighlightBold=True, color={'highlight': highlight},shape='square')
got_net.add_node(dst , dst, title=dst , labelHighlightBold=True, color={'border': "#dd4b39", 'background': "#dd4b39", 'highlight': highlight})
got_net.add_edge(src, dst , value=w, title=w)
neighbor_map = got_net.get_adj_list()
dict = got_net.get_edges()
self.getResourceList()
# add neighbor data to node hover data
for node in got_net.nodes:
counter = 0
if(directed):
node["title"] = "<h3>" + node["title"] + " Output Links: </h3>"
else:
node["title"] = "<h3>" + node["title"] + " Links: </h3>"
for neighbor in neighbor_map[node["id"]]:
if(counter % 10 == 0):
node["title"] += "<br>::: " + neighbor
else:
node["title"] += " ::: " + neighbor
node["value"] = len(neighbor_map[node["id"]])
counter += 1
got_net.show_buttons(filter_=['nodes', 'edges', 'physics'])
got_net.show_buttons(filter_=['physics'])
got_net.show("PMSocial.html")
def interactiveGraphExtended(G):
# plot interactive graph using pyvis, with degree, no of node labeled, size depends on nodes' degree
nt = Network(height="750px", width="100%", bgcolor="#222222", font_color="white")
nt.barnes_hut(spring_strength=0.006)
for node in G:
nt.add_node(node, label=G.degree(node), title="I am node "+str(node), value=G.degree(node))
for edge in G.edges:
nt.add_edge(int(edge[0]), int(edge[1]), color='white')
nt.show("nx.html")
class address_graph:
def __init__(self):
self.graph = Network(height="750px", width="100%", directed=True)
with open('layouts\\cluster_layout.json') as f:
self.composite_options = json.load(f)
def show_graph(self):
dirOutput = "output"
if not os.path.exists(dirOutput):
os.makedirs("output")
self.graph.show("output\\cluster_gragh.html")
def add_address_graph(self, input, output, amount):
input_edge = zip(input, output, amount)
for i in input_edge:
input = i[0]
output = i[1]
weight = i[2]
self.graph.add_node(input)
self.graph.add_node(output)
self.graph.add_edge(input, output, value=weight, title=weight)
self.graph.options = self.composite_options
def colors(self, n):
ret = []
r = int(random.random() * 256)
g = int(random.random() * 256)
b = int(random.random() * 256)
step = 256 / n
for i in range(n):
r += step
g += step
b += step
r = int(r) % 256
g = int(g) % 256
b = int(b) % 256
ret.append((r, g, b))
return ret
def cluster_addresses(self, address, cluster):
color_num = max(cluster)
print(color_num)
colors = self.colors(4)
for i in self.graph.nodes:
try:
idx = address.index(i["id"])
value = cluster[address.index(i["id"])]
print(i, " id ", value)
print(str(colors[value - 1]))
i["color"] = "rgb" + str(colors[value - 1])
except Exception:
pass
def generate_network_plot(species,
path_to_template=template,
path_to_reactions=path):
net = Network(directed=True)
with open(path_to_reactions, 'r') as f:
reactions_data = json.load(f)
contained_reactions = {}
for r in reactions_data['camp-data'][0]['reactions']:
if 'reactants' in r:
tmp = reactions_data['camp-data'][0]['reactions']
if species in r['reactants']:
contained_reactions.update({tmp.index(r): {}})
if species in r['products']:
contained_reactions.update({tmp.index(r): {}})
logging.debug(contained_reactions)
nodes = {}
edges = []
if contained_reactions:
for i in contained_reactions:
tmp = reactions_data['camp-data'][0]['reactions']
reac_data = tmp[i]['reactants']
prod_data = tmp[i]['products']
reactants = [x for x in reac_data]
products = [x for x in prod_data]
first = '+'.join(reactants)
second = '+'.join(products)
name = first + '->' + second
net.add_node(name,
label=name,
color='green',
borderWidthSelected=3)
for j in reactants:
nodes.update({j: {}})
edges.append([j, name])
for k in products:
nodes.update({k: {}})
edges.append([name, k])
else:
net.add_node(
species,
label=species,
)
if species in nodes:
nodes.pop(species)
net.add_node(species, label=species, color='blue', size=50)
for n in nodes:
net.add_node(n, label=n, borderWidthSelected=3, size=40)
for e in edges:
net.add_edge(e[0], e[1])
net.force_atlas_2based(gravity=-100, overlap=1)
net.show(str(path_to_template))
def dynamic_netShow(gnetdata, filename, node_size=50, node_community='all', html_size=["500px", "1800px"],
bgcolor="#222222", font_color="white", **kwarg):
"""
create a GRN html
------------------------------------------
:param gnetdata: Gnetdata object
:param filename: str, save as filename
:param node_size: int, default 50.
:param node_community: str or list, default all.
:param html_size: list, default ["1200px", "1600px"]
:param font_color: string, default white
:param bgcolor: string, default #222222
:return: None
"""
assert 'graph' in gnetdata.NetAttrs.keys(), 'graph is empty!'
assert 'communities' in gnetdata.NetAttrs.keys(), 'node communities is empty!'
node_group = gnetdata.NetAttrs['communities']
graph = gnetdata.NetAttrs['graph']
net = Network(html_size[0], html_size[1], bgcolor=bgcolor, font_color=font_color, **kwarg)
edge_data = zip(list(graph.edges), list(graph[x[0]][x[1]]['weight'] for x in graph.edges))
colors = sns.color_palette().as_hex() + sns.color_palette('Paired', 100).as_hex()
for e in edge_data:
src = e[0][0]
dst = e[0][1]
w = e[1]
if node_community == 'all':
src_color = int(node_group[node_group['node'] == src]['group'])
dst_color = int(node_group[node_group['node'] == dst]['group'])
else:
sub_node_group = node_group[node_group.group.isin(node_community)]
src_color = int(sub_node_group[sub_node_group['node'] == src]['group']) if src in list(
sub_node_group.node) else 'grey'
dst_color = int(sub_node_group[sub_node_group['node'] == dst]['group']) if dst in list(
sub_node_group.node) else 'grey'
net.add_node(src, src, title=src, color='grey' if src_color == 'grey' else colors[src_color])
net.add_node(dst, dst, title=dst, color='grey' if dst_color == 'grey' else colors[dst_color])
net.add_edge(src, dst, value=w)
neighbor_map = net.get_adj_list()
# add neighbor data to node hover data
for node in net.nodes:
node["title"] += " Neighbors:<br>" + "<br>".join(neighbor_map[node["id"]])
node["value"] = len(neighbor_map[node["id"]])
node['size'] = node_size
net.show_buttons(filter_='physics')
net.show(filename)
return None
def show(self, file="state_graph.html", physics=True):
from pyvis.network import Network
net = Network()
for (i, j), weight in self.edges.items():
net.add_node(i)
net.add_node(j)
net.add_edge(i, j, value=weight)
net.toggle_physics(physics)
net.show(file)
def main():
net = Network(height=600, width=900)
net.barnes_hut()
dbName = "pcapDb"
if (not os.path.exists(dbName)):
conn = sqlite3.connect(dbName)
conn.execute(
"""create table packetdata (src text,dst text,len integer);""")
else:
conn = sqlite3.connect(dbName)
cursor = conn.cursor()
header_struct = struct.Struct('!I')
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
sock.bind(("localhost", 9888))
sock.listen(1)
q = queue.Queue()
reciever, _ = sock.accept()
t = threading.Thread(target=display, args=(q, net))
# t.start()
while (True):
data_len = recvall(reciever, header_struct.size)
(data_len, ) = header_struct.unpack(data_len)
data = recvall(reciever, data_len)
data = pickle.loads(data)
# print(data)
nodes = set()
for i in data:
if (i is None):
continue
src, dst, length = i
# print(type(i))
cursor.execute(
"insert into packetdata (src,dst,len) values(?,?,?)",
(src, dst, length))
nodes.add(src)
nodes.add(dst)
weights = []
# print("Here")
for i in nodes:
la = "IP: " + i
net.add_node(i, label=i, title=la)
for i in data:
if (i is None):
continue
src, dst, weight = i
net.add_edge(src, dst, value=weight)
net.write_html("index.html")
time.sleep(4)
def new_draw(self):
"""
draw the ARN using the class attributes
Args:
nothing
Returns:
a local generated web page
"""
got_net = Network(height="750px",
width="100%",
bgcolor="#222222",
font_color="white")
got_net.heading = "Nucleotids"
# set the physics layout of the network
got_net.barnes_hut()
cp = 0
for nuk in self.list_nucleotide:
for tuples in nuk.tup:
if tuples.relation in self.grps.keys():
relation_type = self.grps.get(tuples.relation)
else:
relation_type = 0
relation_type = str(nuk.paired_type)
got_net.add_node(tuples.tup[0],
label="(" + str(tuples.tup[0]) + ")" +
" -> " + str(tuples.tup[1]) + " : " +
str(relation_type),
group=relation_type)
got_net.add_node(tuples.tup[1],
label="(" + str(tuples.tup[1]) + ")" +
" -> " + str(tuples.tup[0]) + " : " +
str(relation_type),
group=relation_type)
got_net.add_edge(tuples.tup[0], tuples.tup[1])
cp += 1
# got_net.add_node(src, src, title=src)
# got_net.add_node(dst, dst, title=dst)
# got_net.add_edge(src, dst, value=w)
# neighbor_map = got_net.get_adj_list()
# add neighbor data to node hover data
'''for node in got_net.nodes:
node["title"] += " Neighbors:<br>" + \
"<br>".join(neighbor_map[node["id"]])
node["value"] = len(neighbor_map[node["id"]])'''
got_net.show("networkRNA.html")
