py2cytoscape wrappers - initial commit

New module to facilitate import of CATMAID networks to Cytoscape.

pymaid/cytoscape.py

@@ -0,0 +1,140 @@
+#    This script is part of pymaid (http://www.github.com/schlegelp/pymaid).
+#    Copyright (C) 2017 Philipp Schlegel
+#
+#   This program is free software: you can redistribute it and/or modify
+#   it under the terms of the GNU General Public License as published by
+#   the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along
+
+""" Set of functions to interface with Cytoscape using its CyREST API. This
+module requires py2cytoscape (https://github.com/cytoscape/py2cytoscape)
+"""
+
+import logging
+
+import networkx as nx
+
+import numpy as np
+import pandas as pd
+
+from py2cytoscape.data.cyrest_client import CyRestClient
+
+# Set up logging
+module_logger = logging.getLogger(__name__)
+module_logger.setLevel(logging.INFO)
+if len( module_logger.handlers ) == 0:
+    # Generate stream handler
+    sh = logging.StreamHandler()
+    sh.setLevel(logging.INFO)
+    # Create formatter and add it to the handlers
+    formatter = logging.Formatter(
+                '%(levelname)-5s : %(message)s (%(name)s)')
+    sh.setFormatter(formatter)
+    module_logger.addHandler(sh)
+
+def get_client():
+    """Initialises connection with Cytoscape and returns client."""
+    return CyRestClient()
+
+def get_pymaid_style():
+    """Returns our default network style."""
+
+    cy = get_client()
+
+    all_styles = cy.style.get_all()
+    s = cy.style.create('pymaid')
+
+    # If the style already existed, return unchanged
+    if 'pymaid' in all_styles:
+        return s
+
+    # If we created the style from scratch, apply some basic settings
+    basic_settings = dict(
+        # You can set default values as key-value pairs.
+
+        NODE_FILL_COLOR= '#FEC44F',
+        NODE_SIZE= 18,
+        NODE_BORDER_WIDTH= 7,
+        NODE_BORDER_COLOR= '#999999',
+        NODE_LABEL_COLOR= '#555555',
+        NODE_LABEL_FONT_SIZE= 14,
+        NODE_LABEL_POSITION= 'S,NW,c,0.00,3.00',
+
+        EDGE_WIDTH= 2,
+        EDGE_TRANSPARENCY= 100,
+        EDGE_CURVED= True,
+        EDGE_BEND= '0.728545744495502,-0.684997151948455,0.6456513365424503',
+        EDGE_UNSELECTED_PAINT= '#CCCCCC',
+        EDGE_STROKE_UNSELECTED_PAINT= '#333333',
+        EDGE_TARGET_ARROW_SHAPE= 'DELTA',
+
+        NETWORK_BACKGROUND_PAINT= '#FFFFFF',
+    )
+
+    s.update_defaults(basic_settings)
+
+    return s
+
+def generate_network(x, clear_session=True):
+    """ Loads a CATMAID network into Cytoscape.
+
+    Parameters
+    ----------
+    x :             {networkx.Graph, pandas.DataFrame}
+                    Network to export to Cytoscape. Can be:
+                      1. NetworkX Graph e.g. from pymaid.networkx (preferred!)
+                      2. Pandas DataFrame. Mandatory columns:
+                         'source','target','interaction'
+    clear_session : bool, optional
+                    If True, will clear session before adding network.
+
+    Returns
+    -------
+    cytoscape Network
+    """
+
+    # Initialise connection with Cytoscape
+    cy = get_client()
+
+    # Clear session
+    if clear_session:
+        cy.session.delete()
+
+    if isinstance(x, nx.Graph ):
+        n = cy.network.create_from_networkx(x)
+    elif isinstance(x, np.ndarray):
+        n = cy.network.create_from_ndarray(x)
+    elif isinstance(x, pd.DataFrame):
+        n = cy.network.create_from_dataframe(x)
+    else:
+        raise TypeError('Unable to generate network from data of type "{0}"'.format(type(x)))
+
+    # Apply basic layout
+    cy.layout.apply(name='degree-circle', network=n)
+
+    # Get our default style
+    s = get_pymaid_style()
+
+    # Add some passthough mappings to the style
+    s.create_passthrough_mapping(column='neuron_name', vp='NODE_LABEL', col_type='String')
+    max_edge_weight = n.get_edge_column('weight').max()
+    s.create_continuous_mapping(column='weight', vp='EDGE_WIDTH', col_type='Double',
+                                points=[{'equal': '1.0', 'greater': '1.0', 'lesser': '1.0', 'value': 1.0},
+                                        {'equal': max_edge_weight/3, 'greater': 1.0, 'lesser': max_edge_weight/3, 'value': max_edge_weight}]
+                                )
+
+    # Apply style
+    cy.style.apply(s, n)
+
+    return n
+
+
+