kantale/cytoscape.py

## cytoscape.py
def cytoscape_nodes(nodes):

	ret = []
	for n in nodes:
		ret.append("{ data: { id: '%s', name: '%s' } }" % (n['id'], n['name']))

	print ('NODES: {}'.format(len(ret)))
	return ',\n'.join(ret) + '\n'

def cytoscape_edges(edges, remove_duplicate_edges = False):


	types = {
		'str' : lambda x : "'%s'" % (x),
		'unicode': lambda x : "'%s'" % (x),
		'int': lambda x : "%s" % (x),
		'float': lambda x : "%s" % (x),
	}

	ret = []
	# 	ret.append("{ data: { source: '%s', target: '%s', xyz: '%s', jaccard: %s } }")
	edge_keys = {}
	duplicate_edges = 0
	for e in edges:
		if remove_duplicate_edges:
			edge_key = '$$'.join(sorted([e['source'], e['target']]))
			if edge_key in edge_keys:
				duplicate_edges += 1
				continue
			else:
				edge_keys[edge_key] = None

		e_data = ", ".join(["%s: %s" % (k, types[type(v).__name__](v))  for k,v in e.items()])
		ret.append("{ data: { %s } }" % (e_data))

	if remove_duplicate_edges:
		print ('Duplicate edges: {}'.format(duplicate_edges))
	print ('EDGES: {}'.format(len(ret)))
	return ', \n'.join(ret) + '\n'


def cytoscape(nodes, edges, output_filename, remove_duplicate_edges=False):
	'''
	idealEdgeLength: function( edge ){ return 500.0 * edge.data('jaccard'); }

	curve-style: bezier, haystack

	.selector('node'):
       'text-outline-width': 2,
        'background-color': '#999',
        'text-outline-color': '#999'

	.selector('edge')
        'target-arrow-shape': 'triangle',
        'target-arrow-color': '#ccc',


    nodes = [{'name': ..., 'id': '...'}]
    edges = [{'source': ... 'target': ...., 'label': ...OPTIONAL...}]

	'''

	nodes_html = cytoscape_nodes(nodes)
	edges_html = cytoscape_edges(edges, remove_duplicate_edges=remove_duplicate_edges)
	labels_html = "'label': 'data(label)'," if 'label' in edges[0].keys() else ''

	html = '''
<!DOCTYPE html>
<!-- This code is for demonstration purposes only.  You should not hotlink to Github, Rawgit, or files from the Cytoscape.js documentation in your production apps. -->
<html>
  <head>
    <meta name="description" content="[An example of getting started with Cytoscape.js]" />
    <style>

body {
  font: 14px helvetica neue, helvetica, arial, sans-serif;
}

#cy {
  height: 100%;
  width: 100%;
  position: absolute;
  left: 0;
  top: 0;
}

#info {
  color: #c88;
  font-size: 1em;
  position: absolute;
  z-index: -1;
  left: 1em;
  top: 1em;
}

    </style>
    <meta charset=utf-8 />
    <meta name="viewport" content="user-scalable=no, initial-scale=1.0, minimum-scale=1.0, maximum-scale=1.0, minimal-ui">
    <title>Cytoscape.js initialisation</title>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.2.3/cytoscape.min.js"></script>
  </head>
  <body>
    <div id="cy"></div>
    <!-- Load appplication code at the end to ensure DOM is loaded -->
    <script>
var cy = cytoscape({
  container: document.querySelector('#cy'),

  boxSelectionEnabled: false,
  autounselectify: true,

  style: cytoscape.stylesheet()
    .selector('node')
      .css({
        'content': 'data(name)',
        'text-valign': 'center',
        'color': 'black'
      })
    .selector('edge')
      .css({
        'curve-style': 'haystack',
        'line-color': '#000',
        $$LABELS$$
        'width': 1
      })
    .selector(':selected')
      .css({
        'background-color': 'black',
        'line-color': 'black',
        'target-arrow-color': 'black',
        'source-arrow-color': 'black'
      })
    .selector('.faded')
      .css({
        'opacity': 0.25,
        'text-opacity': 0
      }),

  elements: {
    nodes: [
     $$NODES$$
    ],
    edges: [
     $$EDGES$$
    ]
  },

  layout: {
        name: 'cose',
        nodeOverlap: 20,
        refresh: 20,
        fit: true,
        padding: 30,
        randomize: false,
        componentSpacing: 100,
        nodeRepulsion: 400000,
        edgeElasticity: 100,
        nestingFactor: 5,
        gravity: 80,
        numIter: 1000,
        initialTemp: 200,
        coolingFactor: 0.95,
        minTemp: 1.0,
        idealEdgeLength: 100
  }
});

cy.on('tap', 'node', function(e){
  var node = e.cyTarget;
  var neighborhood = node.neighborhood().add(node);

  cy.elements().addClass('faded');
  neighborhood.removeClass('faded');
});

cy.on('tap', function(e){
  if( e.cyTarget === cy ){
    cy.elements().removeClass('faded');
  }
});


    </script>
  </body>
</html>

'''.replace('$$NODES$$', nodes_html).replace('$$EDGES$$', edges_html).replace('$$LABELS$$', labels_html)

	print ('Saving cytoscape to: {}'.format(output_filename))
	with open(output_filename, 'w') as f:
		f.write(html)
	def cytoscape_nodes(nodes):

	ret = []
	for n in nodes:
	ret.append("{ data: { id: '%s', name: '%s' } }" % (n['id'], n['name']))

	print ('NODES: {}'.format(len(ret)))
	return ',\n'.join(ret) + '\n'

	def cytoscape_edges(edges, remove_duplicate_edges = False):


	types = {
	'str' : lambda x : "'%s'" % (x),
	'unicode': lambda x : "'%s'" % (x),
	'int': lambda x : "%s" % (x),
	'float': lambda x : "%s" % (x),
	}

	ret = []
	# ret.append("{ data: { source: '%s', target: '%s', xyz: '%s', jaccard: %s } }")
	edge_keys = {}
	duplicate_edges = 0
	for e in edges:
	if remove_duplicate_edges:
	edge_key = '$$'.join(sorted([e['source'], e['target']]))
	if edge_key in edge_keys:
	duplicate_edges += 1
	continue
	else:
	edge_keys[edge_key] = None

	e_data = ", ".join(["%s: %s" % (k, types[type(v).__name__](v)) for k,v in e.items()])
	ret.append("{ data: { %s } }" % (e_data))

	if remove_duplicate_edges:
	print ('Duplicate edges: {}'.format(duplicate_edges))
	print ('EDGES: {}'.format(len(ret)))
	return ', \n'.join(ret) + '\n'


	def cytoscape(nodes, edges, output_filename, remove_duplicate_edges=False):
	'''
	idealEdgeLength: function( edge ){ return 500.0 * edge.data('jaccard'); }

	curve-style: bezier, haystack

	.selector('node'):
	'text-outline-width': 2,
	'background-color': '#999',
	'text-outline-color': '#999'

	.selector('edge')
	'target-arrow-shape': 'triangle',
	'target-arrow-color': '#ccc',


	nodes = [{'name': ..., 'id': '...'}]
	edges = [{'source': ... 'target': ...., 'label': ...OPTIONAL...}]

	'''

	nodes_html = cytoscape_nodes(nodes)
	edges_html = cytoscape_edges(edges, remove_duplicate_edges=remove_duplicate_edges)
	labels_html = "'label': 'data(label)'," if 'label' in edges[0].keys() else ''

	html = '''
	<!DOCTYPE html>
	<!-- This code is for demonstration purposes only. You should not hotlink to Github, Rawgit, or files from the Cytoscape.js documentation in your production apps. -->
	<html>
	<head>
	<meta name="description" content="[An example of getting started with Cytoscape.js]" />
	<style>

	body {
	font: 14px helvetica neue, helvetica, arial, sans-serif;
	}

	#cy {
	height: 100%;
	width: 100%;
	position: absolute;
	left: 0;
	top: 0;
	}

	#info {
	color: #c88;
	font-size: 1em;
	position: absolute;
	z-index: -1;
	left: 1em;
	top: 1em;
	}

	</style>
	<meta charset=utf-8 />
	<meta name="viewport" content="user-scalable=no, initial-scale=1.0, minimum-scale=1.0, maximum-scale=1.0, minimal-ui">
	<title>Cytoscape.js initialisation</title>
	<script src="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.2.3/cytoscape.min.js"></script>
	</head>
	<body>
	<div id="cy"></div>
	<!-- Load appplication code at the end to ensure DOM is loaded -->
	<script>
	var cy = cytoscape({
	container: document.querySelector('#cy'),

	boxSelectionEnabled: false,
	autounselectify: true,

	style: cytoscape.stylesheet()
	.selector('node')
	.css({
	'content': 'data(name)',
	'text-valign': 'center',
	'color': 'black'
	})
	.selector('edge')
	.css({
	'curve-style': 'haystack',
	'line-color': '#000',
	$$LABELS$$
	'width': 1
	})
	.selector(':selected')
	.css({
	'background-color': 'black',
	'line-color': 'black',
	'target-arrow-color': 'black',
	'source-arrow-color': 'black'
	})
	.selector('.faded')
	.css({
	'opacity': 0.25,
	'text-opacity': 0
	}),

	elements: {
	nodes: [
	$$NODES$$
	],
	edges: [
	$$EDGES$$
	]
	},

	layout: {
	name: 'cose',
	nodeOverlap: 20,
	refresh: 20,
	fit: true,
	padding: 30,
	randomize: false,
	componentSpacing: 100,
	nodeRepulsion: 400000,
	edgeElasticity: 100,
	nestingFactor: 5,
	gravity: 80,
	numIter: 1000,
	initialTemp: 200,
	coolingFactor: 0.95,
	minTemp: 1.0,
	idealEdgeLength: 100
	}
	});

	cy.on('tap', 'node', function(e){
	var node = e.cyTarget;
	var neighborhood = node.neighborhood().add(node);

	cy.elements().addClass('faded');
	neighborhood.removeClass('faded');
	});

	cy.on('tap', function(e){
	if( e.cyTarget === cy ){
	cy.elements().removeClass('faded');
	}
	});


	</script>
	</body>
	</html>

	'''.replace('$$NODES$$', nodes_html).replace('$$EDGES$$', edges_html).replace('$$LABELS$$', labels_html)

	print ('Saving cytoscape to: {}'.format(output_filename))
	with open(output_filename, 'w') as f:
	f.write(html)