python-igraph API reference

List of all classes, functions and methods in python-igraph

igraph.drawing.graph.CytoscapeGraphDrawer

class documentation

class CytoscapeGraphDrawer(AbstractXMLRPCDrawer, AbstractGraphDrawer):

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Graph drawer that sends/receives graphs to/from Cytoscape using CytoscapeRPC.

This graph drawer cooperates with Cytoscape using CytoscapeRPC. You need to install the CytoscapeRPC plugin first and start the XML-RPC server on a given port (port 9000 by default) from the appropriate Plugins submenu in Cytoscape.

Graph, vertex and edge attributes are transferred to Cytoscape whenever possible (i.e. when a suitable mapping exists between a Python type and a Cytoscape type). If there is no suitable Cytoscape type for a Python type, the drawer will use a string attribute on the Cytoscape side and invoke str() on the Python attributes.

If an attribute to be created on the Cytoscape side already exists with a different type, an underscore will be appended to the attribute name to resolve the type conflict.

You can use the network_id attribute of this class to figure out the network ID of the last graph drawn with this drawer.

Static Method infer_cytoscape_type Returns a Cytoscape type that can be used to represent all the values in values and an appropriately converted copy of values that is suitable for an XML-RPC call. Note that the string type in Cytoscape is used as a catch-all type; if no other type fits, attribute values will be converted to string and then posted to Cytoscape.
Method __init__ Constructs a Cytoscape graph drawer using the XML-RPC interface of Cytoscape at the given URL.
Method draw Sends the given graph to Cytoscape as a new network.
Method fetch Fetches the network with the given name from Cytoscape.
Instance Variable network_id Undocumented

Inherited from AbstractXMLRPCDrawer:

Instance Variable server Undocumented
Instance Variable service Undocumented
Static Method _resolve_hostname Parses the given URL, resolves the hostname to an IP address and returns a new URL with the resolved IP address. This speeds up things big time on Mac OS X where an IP lookup would be performed for every XML-RPC call otherwise.

Inherited from AbstractGraphDrawer (via AbstractXMLRPCDrawer):

Method ensure_layout Helper method that ensures that layout is an instance of Layout. If it is not, the method will try to convert it to a Layout according to the following rules:
@staticmethod
def infer_cytoscape_type(values):

Returns a Cytoscape type that can be used to represent all the values in values and an appropriately converted copy of values that is suitable for an XML-RPC call. Note that the string type in Cytoscape is used as a catch-all type; if no other type fits, attribute values will be converted to string and then posted to Cytoscape.

None entries are allowed in values, they will be ignored on the Cytoscape side.

def __init__(self, url='http://localhost:9000/Cytoscape'):
overrides igraph.drawing.baseclasses.AbstractXMLRPCDrawer.__init__

Constructs a Cytoscape graph drawer using the XML-RPC interface of Cytoscape at the given URL.

def draw(self, graph, name='Network from igraph', create_view=True, *args, **kwds):
overrides igraph.drawing.graph.AbstractGraphDrawer.draw

Sends the given graph to Cytoscape as a new network.

Parameters
graphUndocumented
namethe name of the network in Cytoscape.
create_viewwhether to create a view for the network in Cytoscape.The default is True.
*argsUndocumented
**kwdsUndocumented
node_idsspecifies the identifiers of the nodes to be used in Cytoscape. This must either be the name of a vertex attribute or a list specifying the identifiers, one for each node in the graph. The default is None, which simply uses the vertex index for each vertex.
def fetch(self, name=None, directed=False, keep_canonical_names=False):

Fetches the network with the given name from Cytoscape.

When fetching networks from Cytoscape, the canonicalName attributes of vertices and edges are not converted by default. Use the keep_canonical_names parameter to retrieve these attributes as well.

Parameters
namethe name of the network in Cytoscape.
directedwhether the network is directed.
keep_canonical_nameswhether to keep the canonicalName vertex/edge attributes that are added automatically by Cytoscape
Returns
an appropriately constructed igraph Graph.
network_id =

Undocumented