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IPyCytoscape Example

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IPyCytoscape Example#

Thebe can display output from ipycytoscape, which could visualize graphs using Cytoscape.js.

Setup#

Be sure to load require.js before any of your thebe activation code so that the Cytoscape visualizations can function:

<script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>

Configure thebe and load it:

<script type="text/x-thebe-config">
  {
    requestKernel: true,
    binderOptions: {
      repo: "QuantStack/ipycytoscape",
      ref: "1.2.0",
      repoProvider: "github",
    },
  }
</script>
<script src="https://unpkg.com/thebe@latest/lib/index.js"></script>

Create a button to activate thebe:

<button id="activateButton" style="width: 120px; height: 40px; font-size: 1.5em;">
  Activate
</button>
<script>
var bootstrapThebe = function() {
    thebe.bootstrap();
}
document.querySelector("#activateButton").addEventListener('click', bootstrapThebe)
</script>

Now add code cells between these HTML tags:

<pre data-executable="true" data-language="python"></pre>

Example#

Using Cytoscape, you can display a graph with several nodes. This example is from the ipycytoscape repository and is licensed under the BSD 3-Clause License.

Press the “Activate” button below to connect to a Jupyter server:

import ipycytoscape
data = {
  'nodes': [
      { 'data': { 'id': 'desktop', 'name': 'Cytoscape', 'href': 'http://cytoscape.org' } },
      { 'data': { 'id': 'a', 'name': 'Grid', 'href': 'http://cytoscape.org' } },
      { 'data': { 'id': 'b', 'name': 'Cola', 'href': 'http://cytoscape.org' } },
      { 'data': { 'id': 'c', 'name': 'Popper', 'href': 'http://cytoscape.org' } },
      { 'data': { 'id': 'js', 'name': 'Cytoscape.js', 'href': 'http://js.cytoscape.org' } }
  ],
  'edges': [
      {'data': { 'source': 'desktop', 'target': 'js' }},
      {'data': { 'source': 'a', 'target': 'b' }},
      {'data': { 'source': 'a', 'target': 'c' }},
      {'data': { 'source': 'b', 'target': 'c' }},
      {'data': { 'source': 'js', 'target': 'b' }}
  ]
}
cytoscapeobj = ipycytoscape.CytoscapeWidget()
cytoscapeobj.graph.add_graph_from_json(data)
cytoscapeobj.set_style([{
  'selector': 'node',
  'css': {
      'content': 'data(name)',
      'text-valign': 'center',
      'color': 'white',
      'text-outline-width': 2,
      'text-outline-color': 'green',
      'background-color': 'green'
  }
  },
  {
  'selector': ':selected',
  'css': {
      'background-color': 'black',
      'line-color': 'black',
      'target-arrow-color': 'black',
      'source-arrow-color': 'black',
      'text-outline-color': 'black'
  }}
  ])
cytoscapeobj
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