Added Phylogeny Example

Author: Xing Han Lu

demos/usage-phylogeny.py

@@ -0,0 +1,111 @@
+import dash_cytoscape
+import dash
+from dash.dependencies import Input, Output
+import dash_html_components as html
+import dash_core_components as dcc
+
+try:
+    from Bio import Phylo
+except ModuleNotFoundError as e:
+    print(e, "Please make sure you have biopython installed correctly before running this example.")
+
+
+def generate_elements(tree):
+    elements = []
+
+    def _add_to_elements(clade, clade_id):
+        children = clade.clades
+
+        cy_source = {"data": {"id": clade_id}, 'classes': 'nonterminal'}
+        elements.append(cy_source)
+
+        if clade.is_terminal():
+            cy_source['data']['name'] = clade.name
+            cy_source['classes'] = 'terminal'
+
+        for n, child in enumerate(children, 1):
+            child_id = len(elements) + n
+
+            cy_edge = {'data': {
+                'source': clade_id,
+                'target': child_id,
+                'length': clade.branch_length
+            }}
+
+            if clade.confidence and clade.confidence.value:
+                cy_source['data']['confidence'] = clade.confidence.value
+
+            elements.extend([cy_edge])
+
+            _add_to_elements(child, child_id)
+
+    _add_to_elements(tree.clade, 0)
+
+    return elements
+
+
+# Define elements, stylesheet and layout
+tree = Phylo.read('data/apaf.xml', 'phyloxml')
+elements = generate_elements(tree)
+
+layout = {
+    'name': 'breadthfirst',
+    'directed': True
+}
+
+stylesheet = [
+    {
+        'selector': '.nonterminal',
+        'style': {
+            'label': 'data(confidence)',
+            'background-opacity': 0,
+            "text-halign": "left",
+            "text-valign": "top",
+        }
+    },
+    {
+        'selector': 'edge',
+        'style': {
+            "source-endpoint": "outside-to-node",
+        }
+    },
+    {
+        'selector': '.terminal',
+        'style': {
+            'label': 'data(name)',
+            "shape": "roundrectangle",
+            "width": 115,
+            "height": 25,
+            "text-valign": "center",
+            'background-color': 'white',
+            "border-width": 1.5,
+            "border-style": "solid",
+            "border-opacity": 1,
+        }
+    }
+]
+
+
+# Start the app
+app = dash.Dash(__name__)
+
+app.scripts.config.serve_locally = True
+app.css.config.serve_locally = True
+
+
+app.layout = html.Div([
+    dash_cytoscape.Cytoscape(
+        id='cytoscape',
+        elements=elements,
+        stylesheet=stylesheet,
+        layout=layout,
+        style={
+            'height': '95vh',
+            'width': '100%'
+        }
+    )
+])
+
+
+if __name__ == '__main__':
+    app.run_server(debug=True)