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| <article id="content"> | ||
| <header> | ||
| <h1 class="title">Module <code>likelihood.graph.graph</code></h1> | ||
| </header> | ||
| <section id="section-intro"> | ||
| </section> | ||
| <section> | ||
| </section> | ||
| <section> | ||
| </section> | ||
| <section> | ||
| </section> | ||
| <section> | ||
| <h2 class="section-title" id="header-classes">Classes</h2> | ||
| <dl> | ||
| <dt id="likelihood.graph.graph.DynamicGraph"><code class="flex name class"> | ||
| <span>class <span class="ident">DynamicGraph</span></span> | ||
| <span>(</span><span>df: pandas.core.frame.DataFrame, n_importances: int, **kwargs)</span> | ||
| </code></dt> | ||
| <dd> | ||
| <details class="source"> | ||
| <summary> | ||
| <span>Expand source code</span> | ||
| </summary> | ||
| <pre><code class="python">class DynamicGraph(FeatureSelection): | ||
| """A class to represent a dynamic graph""" | ||
|
|
||
| def __init__(self, df: DataFrame, n_importances: int, **kwargs): | ||
| self.G = Network( | ||
| notebook=True, cdn_resources="remote", directed=True | ||
| ) # enable interactive visualization in Jupyter Notebooks | ||
| self.df = df | ||
| self.n_importances = n_importances | ||
| super().__init__(**kwargs) | ||
| self.labels: List[str] = [] | ||
|
|
||
| def fit(self, **kwargs) -> None: | ||
| """Fit the model according to the given data and parameters.""" | ||
| self.get_digraph(self.df, self.n_importances) | ||
| # create a dictionary with the indexes and names of the dataframe | ||
| self.get_index = dict(zip(self.X.columns, range(len(self.X.columns)))) | ||
| self._make_network() | ||
|
|
||
| def _make_network(self) -> None: | ||
| """Create nodes and edges of the network based on feature importance scores""" | ||
| self._add_nodes() | ||
| for i in range(len(self.all_features_imp_graph)): | ||
| node = self.all_features_imp_graph[i][0] | ||
| edges = self.all_features_imp_graph[i][1] | ||
|
|
||
| for label, weight in edges: | ||
| self.G.add_edge(self.get_index[node], self.get_index[label], weight=weight) | ||
|
|
||
| def _add_nodes(self) -> None: | ||
| for i in range(len(self.all_features_imp_graph)): | ||
| node = self.all_features_imp_graph[i][0] | ||
| self.labels.append(node) | ||
| self.G.add_node(n_id=i, label=node) | ||
|
|
||
| def draw(self, name="graph.html", **kwargs) -> None: | ||
| """Display the network using HTML format""" | ||
| spring_length = kwargs["spring_length"] if "spring_length" in kwargs else 500 | ||
| node_distance = kwargs["node_distance"] if "node_distance" in kwargs else 100 | ||
| self.G.repulsion(node_distance=node_distance, spring_length=spring_length) | ||
| self.G.show_buttons(filter_=["physics"]) | ||
| self.G.show(name) | ||
|
|
||
| html_file_content = open(name, "r").read() | ||
| display(HTML(html_file_content)) | ||
|
|
||
| def pyvis_to_networkx(self): | ||
| nx_graph = nx.Graph() | ||
|
|
||
| # Adding nodes | ||
| nodes = [d["id"] for d in self.G.nodes] | ||
| for node_dic in self.G.nodes: | ||
| id = node_dic["label"] | ||
| del node_dic["label"] | ||
| nx_graph.add_nodes_from([(id, node_dic)]) | ||
| self.node_edge_dict = dict(zip(nodes, self.labels)) | ||
| del nodes | ||
|
|
||
| # Adding edges | ||
| for edge in self.G.edges: | ||
| source, target = self.node_edge_dict[edge["from"]], self.node_edge_dict[edge["to"]] | ||
| del edge["from"] | ||
| del edge["to"] | ||
| nx_graph.add_edges_from([(source, target, edge)]) | ||
|
|
||
| return nx_graph</code></pre> | ||
| </details> | ||
| <div class="desc"><p>A class to represent a dynamic graph</p> | ||
| <p>The initializer of the class. The initial parameter is a list of strings with variables to discard.</p></div> | ||
| <h3>Ancestors</h3> | ||
| <ul class="hlist"> | ||
| <li><a title="likelihood.tools.tools.FeatureSelection" href="../tools/tools.html#likelihood.tools.tools.FeatureSelection">FeatureSelection</a></li> | ||
| </ul> | ||
| <h3>Methods</h3> | ||
| <dl> | ||
| <dt id="likelihood.graph.graph.DynamicGraph.draw"><code class="name flex"> | ||
| <span>def <span class="ident">draw</span></span>(<span>self, name='graph.html', **kwargs) ‑> None</span> | ||
| </code></dt> | ||
| <dd> | ||
| <details class="source"> | ||
| <summary> | ||
| <span>Expand source code</span> | ||
| </summary> | ||
| <pre><code class="python">def draw(self, name="graph.html", **kwargs) -> None: | ||
| """Display the network using HTML format""" | ||
| spring_length = kwargs["spring_length"] if "spring_length" in kwargs else 500 | ||
| node_distance = kwargs["node_distance"] if "node_distance" in kwargs else 100 | ||
| self.G.repulsion(node_distance=node_distance, spring_length=spring_length) | ||
| self.G.show_buttons(filter_=["physics"]) | ||
| self.G.show(name) | ||
|
|
||
| html_file_content = open(name, "r").read() | ||
| display(HTML(html_file_content))</code></pre> | ||
| </details> | ||
| <div class="desc"><p>Display the network using HTML format</p></div> | ||
| </dd> | ||
| <dt id="likelihood.graph.graph.DynamicGraph.fit"><code class="name flex"> | ||
| <span>def <span class="ident">fit</span></span>(<span>self, **kwargs) ‑> None</span> | ||
| </code></dt> | ||
| <dd> | ||
| <details class="source"> | ||
| <summary> | ||
| <span>Expand source code</span> | ||
| </summary> | ||
| <pre><code class="python">def fit(self, **kwargs) -> None: | ||
| """Fit the model according to the given data and parameters.""" | ||
| self.get_digraph(self.df, self.n_importances) | ||
| # create a dictionary with the indexes and names of the dataframe | ||
| self.get_index = dict(zip(self.X.columns, range(len(self.X.columns)))) | ||
| self._make_network()</code></pre> | ||
| </details> | ||
| <div class="desc"><p>Fit the model according to the given data and parameters.</p></div> | ||
| </dd> | ||
| <dt id="likelihood.graph.graph.DynamicGraph.pyvis_to_networkx"><code class="name flex"> | ||
| <span>def <span class="ident">pyvis_to_networkx</span></span>(<span>self)</span> | ||
| </code></dt> | ||
| <dd> | ||
| <details class="source"> | ||
| <summary> | ||
| <span>Expand source code</span> | ||
| </summary> | ||
| <pre><code class="python">def pyvis_to_networkx(self): | ||
| nx_graph = nx.Graph() | ||
|
|
||
| # Adding nodes | ||
| nodes = [d["id"] for d in self.G.nodes] | ||
| for node_dic in self.G.nodes: | ||
| id = node_dic["label"] | ||
| del node_dic["label"] | ||
| nx_graph.add_nodes_from([(id, node_dic)]) | ||
| self.node_edge_dict = dict(zip(nodes, self.labels)) | ||
| del nodes | ||
|
|
||
| # Adding edges | ||
| for edge in self.G.edges: | ||
| source, target = self.node_edge_dict[edge["from"]], self.node_edge_dict[edge["to"]] | ||
| del edge["from"] | ||
| del edge["to"] | ||
| nx_graph.add_edges_from([(source, target, edge)]) | ||
|
|
||
| return nx_graph</code></pre> | ||
| </details> | ||
| <div class="desc"></div> | ||
| </dd> | ||
| </dl> | ||
| <h3>Inherited members</h3> | ||
| <ul class="hlist"> | ||
| <li><code><b><a title="likelihood.tools.tools.FeatureSelection" href="../tools/tools.html#likelihood.tools.tools.FeatureSelection">FeatureSelection</a></b></code>: | ||
| <ul class="hlist"> | ||
| <li><code><a title="likelihood.tools.tools.FeatureSelection.get_digraph" href="../tools/tools.html#likelihood.tools.tools.FeatureSelection.get_digraph">get_digraph</a></code></li> | ||
| </ul> | ||
| </li> | ||
| </ul> | ||
| </dd> | ||
| </dl> | ||
| </section> | ||
| </article> | ||
| <nav id="sidebar"> | ||
| <div class="toc"> | ||
| <ul></ul> | ||
| </div> | ||
| <ul id="index"> | ||
| <li><h3>Super-module</h3> | ||
| <ul> | ||
| <li><code><a title="likelihood.graph" href="index.html">likelihood.graph</a></code></li> | ||
| </ul> | ||
| </li> | ||
| <li><h3><a href="#header-classes">Classes</a></h3> | ||
| <ul> | ||
| <li> | ||
| <h4><code><a title="likelihood.graph.graph.DynamicGraph" href="#likelihood.graph.graph.DynamicGraph">DynamicGraph</a></code></h4> | ||
| <ul class=""> | ||
| <li><code><a title="likelihood.graph.graph.DynamicGraph.draw" href="#likelihood.graph.graph.DynamicGraph.draw">draw</a></code></li> | ||
| <li><code><a title="likelihood.graph.graph.DynamicGraph.fit" href="#likelihood.graph.graph.DynamicGraph.fit">fit</a></code></li> | ||
| <li><code><a title="likelihood.graph.graph.DynamicGraph.pyvis_to_networkx" href="#likelihood.graph.graph.DynamicGraph.pyvis_to_networkx">pyvis_to_networkx</a></code></li> | ||
| </ul> | ||
| </li> | ||
| </ul> | ||
| </li> | ||
| </ul> | ||
| </nav> | ||
| </main> | ||
| <footer id="footer"> | ||
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