j1-template 2022.5.0.rc3 → 2022.5.1.rc0

data/lib/starter_web/pages/public/_jupyter/notebooks/textbooks/j1_bokeh_08_graph_and_network_plots.html

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-<h2 id="8.-Graph-and-Network-Plots">8. Graph and Network Plots<a class="anchor-link" href="#8.-Graph-and-Network-Plots">&#182;</a></h2><p>This chapter will cover how to plot network node/link graphs in Bokeh using NetworkX. For information on creating graph renderers from a low level, see <a href="https://docs.bokeh.org/en/latest/docs/user_guide/graph.html">Visualizing Network Graphs</a></p>
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-<h3 id="Plotting-from-NetworkX">Plotting from NetworkX<a class="anchor-link" href="#Plotting-from-NetworkX">&#182;</a></h3><p>The easiest way to plot network graphs with Bokeh is to use the <code>from_networkx</code> function. This function accepts any NetworkX graph and returns a Bokeh <code>GraphRenderer</code> that can be added to a plot. The <code>GraphRenderer</code> has <code>node_renderer</code> and <code>edge_renderer</code> properties that contain the Bokeh renderers that draw the nodes and edges, respectively.</p>
-<p>The example below shows a Bokeh plot of <code>nx.desargues_graph()</code>, setting some of the node and edge properties.</p>
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-
-<div class="inner_cell">
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
-<span class="kn">from</span> <span class="nn">bokeh.models</span> <span class="kn">import</span> <span class="n">Range1d</span><span class="p">,</span> <span class="n">Plot</span>
-<span class="kn">from</span> <span class="nn">bokeh.plotting</span> <span class="kn">import</span> <span class="n">from_networkx</span>
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-<span class="n">G</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">desargues_graph</span><span class="p">()</span>
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-<span class="c1"># We could use figure here but don&#39;t want all the axes and titles</span>
-<span class="n">plot</span> <span class="o">=</span> <span class="n">Plot</span><span class="p">(</span><span class="n">x_range</span><span class="o">=</span><span class="n">Range1d</span><span class="p">(</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="n">y_range</span><span class="o">=</span><span class="n">Range1d</span><span class="p">(</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">))</span>
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-<span class="c1"># Create a Bokeh graph from the NetworkX input using nx.spring_layout</span>
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-<span class="n">plot</span><span class="o">.</span><span class="n">renderers</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">graph</span><span class="p">)</span>
-
-<span class="c1"># Set some of the default node glyph (Circle) properties</span>
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-
-<span class="c1"># Set some edge properties too</span>
-<span class="n">graph</span><span class="o">.</span><span class="n">edge_renderer</span><span class="o">.</span><span class="n">glyph</span><span class="o">.</span><span class="n">line_dash</span> <span class="o">=</span> <span class="p">[</span><span class="mi">2</span><span class="p">,</span><span class="mi">2</span><span class="p">]</span>
-
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-<h3 id="Adding-Extra-Data-Columns.">Adding Extra Data Columns.<a class="anchor-link" href="#Adding-Extra-Data-Columns.">&#182;</a></h3><p>The <code>node_renderer</code> and <code>edge_renderer</code> properties of the graph renderer each have a <code>data_source</code> that is a standard <code>ColumnDataSource</code> that you can add new data to, e.g. to drive a hover tool, or to specify colors for the renderer. The example below demonstates both.</p>
-
-</div>
-</div>
-</div>
-
-  
-
-  <div class="
-      cell border-box-sizing code_cell rendered">
-    <div class="input">
-
-<div class="inner_cell">
-    <div class="input_area">
-<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">bokeh.models</span> <span class="kn">import</span> <span class="n">HoverTool</span>
-<span class="kn">from</span> <span class="nn">bokeh.palettes</span> <span class="kn">import</span> <span class="n">Category20_20</span>
-
-<span class="n">G</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">desargues_graph</span><span class="p">()</span> <span class="c1"># always 20 nodes</span>
-
-<span class="c1"># We could use figure here but don&#39;t want all the axes and titles</span>
-<span class="n">plot</span> <span class="o">=</span> <span class="n">Plot</span><span class="p">(</span><span class="n">x_range</span><span class="o">=</span><span class="n">Range1d</span><span class="p">(</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="n">y_range</span><span class="o">=</span><span class="n">Range1d</span><span class="p">(</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">))</span>
-
-<span class="c1"># Create a Bokeh graph from the NetworkX input using nx.spring_layout</span>
-<span class="n">graph</span> <span class="o">=</span> <span class="n">from_networkx</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">nx</span><span class="o">.</span><span class="n">spring_layout</span><span class="p">,</span> <span class="n">scale</span><span class="o">=</span><span class="mf">1.8</span><span class="p">,</span> <span class="n">center</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">))</span>
-<span class="n">plot</span><span class="o">.</span><span class="n">renderers</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">graph</span><span class="p">)</span>
-
-<span class="c1"># Add some new columns to the node renderer data source</span>
-<span class="n">graph</span><span class="o">.</span><span class="n">node_renderer</span><span class="o">.</span><span class="n">data_source</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;index&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">G</span><span class="p">)))</span>
-<span class="n">graph</span><span class="o">.</span><span class="n">node_renderer</span><span class="o">.</span><span class="n">data_source</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;colors&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">Category20_20</span>
-
-<span class="n">graph</span><span class="o">.</span><span class="n">node_renderer</span><span class="o">.</span><span class="n">glyph</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span> <span class="n">fill_color</span><span class="o">=</span><span class="s2">&quot;colors&quot;</span><span class="p">)</span>
-
-<span class="n">plot</span><span class="o">.</span><span class="n">add_tools</span><span class="p">(</span><span class="n">HoverTool</span><span class="p">(</span><span class="n">tooltips</span><span class="o">=</span><span class="s2">&quot;index: @index&quot;</span><span class="p">))</span>
-
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-<h3 id="Inspection-and-Selection-Policies">Inspection and Selection Policies<a class="anchor-link" href="#Inspection-and-Selection-Policies">&#182;</a></h3><p>Bokeh graph renderers have <code>inspection_policy</code> and <code>selection_policy</code> properties. These can be used to control how hover inspections highlight the graph, or how selection tools make selections. These properties may be set to any of the inpection policies in <code>bokeh.graphs</code>. For instance, if a user hovers over a node, you may wish to highlight all the associated edges as well. This can be accomplished by setting the inspection policy:</p>
-<div class="highlight"><pre><span></span><span class="n">graph</span><span class="o">.</span><span class="n">inspection_policy</span> <span class="o">=</span> <span class="n">NodesAndLinkedEdges</span><span class="p">()</span>
-</pre></div>
-<p>as the example below demonstrates.</p>
-
-</div>
-</div>
-</div>
-
-  
-
-  <div class="
-      cell border-box-sizing code_cell rendered">
-    <div class="input">
-
-<div class="inner_cell">
-    <div class="input_area">
-<div class=" highlight hl-ipython3"><pre><span></span><span class="kn">from</span> <span class="nn">bokeh.models.graphs</span> <span class="kn">import</span> <span class="n">NodesAndLinkedEdges</span>
-<span class="kn">from</span> <span class="nn">bokeh.models</span> <span class="kn">import</span> <span class="n">Circle</span><span class="p">,</span> <span class="n">HoverTool</span><span class="p">,</span> <span class="n">MultiLine</span>
-
-<span class="n">G</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">gnm_random_graph</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span> <span class="mi">30</span><span class="p">)</span>
-
-<span class="c1"># We could use figure here but don&#39;t want all the axes and titles</span>
-<span class="n">plot</span> <span class="o">=</span> <span class="n">Plot</span><span class="p">(</span><span class="n">x_range</span><span class="o">=</span><span class="n">Range1d</span><span class="p">(</span><span class="o">-</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">),</span> <span class="n">y_range</span><span class="o">=</span><span class="n">Range1d</span><span class="p">(</span><span class="o">-</span><span class="mi">2</span> <span class="p">,</span><span class="mi">2</span><span class="p">))</span>
-
-<span class="c1"># Create a Bokeh graph from the NetworkX input using nx.spring_layout</span>
-<span class="n">graph</span> <span class="o">=</span> <span class="n">from_networkx</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">nx</span><span class="o">.</span><span class="n">spring_layout</span><span class="p">,</span> <span class="n">scale</span><span class="o">=</span><span class="mf">1.8</span><span class="p">,</span> <span class="n">center</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">))</span>
-<span class="n">plot</span><span class="o">.</span><span class="n">renderers</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">graph</span><span class="p">)</span>
-
-<span class="c1"># Blue circles for nodes, and light grey lines for edges</span>
-<span class="n">graph</span><span class="o">.</span><span class="n">node_renderer</span><span class="o">.</span><span class="n">glyph</span> <span class="o">=</span> <span class="n">Circle</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">25</span><span class="p">,</span> <span class="n">fill_color</span><span class="o">=</span><span class="s1">&#39;#2b83ba&#39;</span><span class="p">)</span>
-<span class="n">graph</span><span class="o">.</span><span class="n">edge_renderer</span><span class="o">.</span><span class="n">glyph</span> <span class="o">=</span> <span class="n">MultiLine</span><span class="p">(</span><span class="n">line_color</span><span class="o">=</span><span class="s2">&quot;#cccccc&quot;</span><span class="p">,</span> <span class="n">line_alpha</span><span class="o">=</span><span class="mf">0.8</span><span class="p">,</span> <span class="n">line_width</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
-
-<span class="c1"># green hover for both nodes and edges</span>
-<span class="n">graph</span><span class="o">.</span><span class="n">node_renderer</span><span class="o">.</span><span class="n">hover_glyph</span> <span class="o">=</span> <span class="n">Circle</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">25</span><span class="p">,</span> <span class="n">fill_color</span><span class="o">=</span><span class="s1">&#39;#abdda4&#39;</span><span class="p">)</span>
-<span class="n">graph</span><span class="o">.</span><span class="n">edge_renderer</span><span class="o">.</span><span class="n">hover_glyph</span> <span class="o">=</span> <span class="n">MultiLine</span><span class="p">(</span><span class="n">line_color</span><span class="o">=</span><span class="s1">&#39;#abdda4&#39;</span><span class="p">,</span> <span class="n">line_width</span><span class="o">=</span><span class="mi">4</span><span class="p">)</span>
-
-<span class="c1"># When we hover over nodes, highlight adjecent edges too</span>
-<span class="n">graph</span><span class="o">.</span><span class="n">inspection_policy</span> <span class="o">=</span> <span class="n">NodesAndLinkedEdges</span><span class="p">()</span>
-
-<span class="n">plot</span><span class="o">.</span><span class="n">add_tools</span><span class="p">(</span><span class="n">HoverTool</span><span class="p">(</span><span class="n">tooltips</span><span class="o">=</span><span class="kc">None</span><span class="p">))</span>
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-        if (attempts > 100) {
-          clearInterval(timer);
-          console.log("Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing");
-        }
-      }
-    }, 10, root)
-  }
-})(window);
-</script>
-</div>
-
-</div>
-
-</div>
-</div>
-
-  </div>
-