class CytoscapeGraphDrawer(AbstractXMLRPCDrawer, AbstractGraphDrawer):
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 |
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 |
Undocumented |
Inherited from AbstractXMLRPCDrawer
:
Instance Variable | server |
Undocumented |
Instance Variable | service |
Undocumented |
Static Method | _resolve |
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 |
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: |
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.
Sends the given graph to Cytoscape as a new network.
Parameters | |
graph | Undocumented |
name | the name of the network in Cytoscape. |
create | whether to create a view for the network in Cytoscape.The default is True. |
*args | Undocumented |
**kwds | Undocumented |
node | specifies 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. |
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 | |
name | the name of the network in Cytoscape. |
directed | whether the network is directed. |
keep | whether to keep the canonicalName vertex/edge attributes that are added automatically by Cytoscape |
Returns | |
an appropriately constructed igraph Graph . |