cyclient.network.rename
cyclient.network.rename(self, name=None, sourceNetwork=None, verbose=False)
Rename an existing network. The SUID of the network is returned
name (string)
Enter a new title for the networksourceNetwork (string)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.-
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returns
SUID of the network is returned
cyclient.network.import_url
cyclient.network.import_url(self, dataTypeList=None, defaultInteraction=None, delimiters=None, delimitersForDataList=None, firstRowAsColumnNames=None, \ indexColumnSourceInteraction=None, indexColumnTargetInteraction=None, indexColumnTypeInteraction=None, \ NetworkViewRendererList=None, RootNetworkList=None, startLoadRow=None,\ TargetColumnList=None, url=None, verbose=False)
Import a new network from a tabular formatted file type (e.g. csv, tsv, Excel, etc.). Use network load file to load network formatted files. This command will create a new network collection if no current network collection is selected, otherwise it will add the network to the current collection. The SUIDs of the new networks and views are returned.
dataTypeList (string, optional)
List of column data types ordered by column index (e.g. "string,int,long,double,boolean,intlist" or just "s,i,l,d,b,il"): ,defaultInteraction (string, optional)
Used to set the default interaction type to use when there is no interaction type column.delimiters (string, optional)
Select the delimiters to use to separate columns in the table, from the list ',',' ','TAB', or ';'. TAB and ',' are used by default = [',', ';', ' ', '\t']delimitersForDataList (string, optional)
Select the delimiters to use to separate list entries in a list, from the list '|','\','/', or ','. | is used by default = ['|', '\', '/', ',']firstRowAsColumnNames (string, optional)
If this is true then the first row should contain the names of the columns. Note that startLoadRow must be set for this to work properlyindexColumnSourceInteraction (string)
The column index that contains the source node identifiers.indexColumnTargetInteraction (string, optional)
The column index that contains the target node identifiers. If this is not specified then the resulting network will have no edgesindexColumnTypeInteraction (string, optional)
The column index that contains the interaction type. This is not required.NetworkViewRendererList (string, optional)
Enter the network view renderer that this network should use. This is only useful if multiple renderers have been installed, which is rare. = ['']RootNetworkList (string, optional)
The name of the network collection (root network) that the imported network should be part of. A name of -- Create new network collection -- will result in the creation of a new network collection for this import. = ['-- Create new network collection --', 'cy:command_documentation_generation']startLoadRow (string, optional)
The starting row of the import. This is used to skip over comments and other non-data rows at the beginning of the file.TargetColumnList (string, optional)
Enter the name of the column in the existing network collection (root network) that you want to map your input identifiers to. = ['']url (string)
The URL of the file or resource that provides the table or network to be imported.-
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returns
{ SUIDs of the new networks and views }
cyclient.network.add_node
cyclient.network.add_node(self, name=None,network=None, verbose=False)
Add a new node to an existing network. The name of the node must be provided.
name (string, optional)
The name of the node, which will be assigned to both the 'name' and 'shared name' columnsnetwork (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.-
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returns
node SUID
cyclient.network.list_properties
cyclient.network.list_properties(self, network=None, verbose=False)
List all of the visual properties for networks.
network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.-
verbose
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returns
[ List all of the visual properties ]
cyclient.network.get_porperties
cyclient.network.get_porperties(self, network=None, propertyList=None, verbose=False)
Returns the visual properties for the network that matches the passed parameters.
network (string)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.propertyList (string)
A comma-separated list of network properties-
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returns
visual properties for the network that matches the passed parameters
cyclient.network.export
cyclient.network.export(self, options=None, OutputFile=None, verbose=False)
Export a network to a network file (e.g. XGMML, SIF, etc.)
options (string, optional)
The format of the output file. = ['CX JSON (.cx)', 'Cytoscape.js JSON (.cyjs)', 'GraphML files (.graphml, .xml)', 'NNF (.nnf)', 'PSI-MI Level 1', 'PSI-MI Level 2.5', 'SIF (.sif)', 'XGMML (.xgmml, .xml)']OutputFile (string, optional)
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returns
{ file }
cyclient.network.select
cyclient.network.select(self, adjacentEdges=None, edgeList=None, extendEdges=None, firstNeighbors=None, invert=None, network=None, nodeList=None, verbose=False)
Select nodes and/or edges in a network. This command provides options to invert the selection, add first neighbors, add adjacent edges of selected nodes, and add adjacent nodes of selected edges
adjacentEdges (string, optional)
If 'true', then select any edges adjacent to any selected nodes. This happens before any inversionedgeList (string, optional)
Specifies a list of edges. The keywords all, selected, or unselected can be used to specify edges by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.extendEdges (string, optional)
If 'true', then select any nodes adjacent to any selected edges. This happens before any inversionfirstNeighbors (string, optional)
If this option is anything other than 'none', add nodes to the selection based on the value of the argument. If 'incoming', add nodes to the selection that have edges pointing to one of the selected nodes. If 'output', add nodes to the selection that have edges that point to them from one of the selected nodes. If 'undirected' add any neighbors that have undirected edges connecting to any of the selected nodes. Finally, if 'any', then add all first neighbors to the selection list. = ['none', 'incoming', 'outgoing', 'undirected', 'any'],invert (string, optional)
If this option is not 'none', then the selected nodes or edges (or both) will be deselected and all other nodes or edges will be selected = ['none', 'nodes', 'edges', 'both']network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.nodeList (string, optional)
Specifies a list of nodes. The keywords all, selected, or unselected can be used to specify nodes by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.-
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returns
[ list of selected edges and nodes ]
cyclient.network.deselect
cyclient.network.deselect(self, edgeList=None, network=None, nodeList=None, verbose=False)
Deselect nodes and/or edges in a network. A list of nodes and/or edges may be provided and those nodes and edges will be deselected.
edgeList (string, optional)
Specifies a list of edges. The keywords all, selected, or unselected can be used to specify edges by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.nodeList (string, optional)
Specifies a list of nodes. The keywords all, selected, or unselected can be used to specify nodes by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.verbose
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:retunrs: [ list of deselected nodes and edges ]
cyclient.network.hide
cyclient.network.hide(self, edgeList=None, network=None, nodeList=None, verbose=False)
Hide nodes and/or edges in a network. A list of nodes and/or edges may be provided and those nodes and edges will be hidden in the view associated with the provided network.Note that the network '''must''' have a view. The SUIDs of the hidden nodes and/or edges are returned.
edgeList (string, optional)
Specifies a list of edges. The keywords all, selected, or unselected can be used to specify edges by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.nodeList (string, optional)
Specifies a list of nodes. The keywords all, selected, or unselected can be used to specify nodes by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.-
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returns
[ list of SUIDs of the hidden nodes and/or edges ]
cyclient.network.load_url
cyclient.network.load_url(self, afile=None, verbose=False)
Load a new network from a URL that points to a network file type (e.g. SIF, XGMML, etc.). Use network import url to load networks from Excel or csv files. This command will create a new network collection if no current network collection is selected, otherwise it will add the network to the current collection. The SUIDs of the new networks and views are returned.
url (string)
Select a URL that points to a network format file. This command does not support csv or Excel files. Use network import url for that.-
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returns
{ SUIDs of the new networks and views }
cyclient.network.create
cyclient.network.create(self, edgeList=None, excludeEdges=None, networkName=None, nodeList=None, source=None, verbose=False)
Create a new network from a list of nodes and edges in an existing source network. The SUID of the network and view are returned.
edgeList (string, optional)
Specifies a list of edges. The keywords all, selected, or unselected can be used to specify edges by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.excludeEdges (string, optional)
Unless this is set to true, edges that connect nodes in the nodeList are implicitly includednetworkName (string, optional)
nodeList (string, optional)
Specifies a list of nodes. The keywords all, selected, or unselected can be used to specify nodes by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.source (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.-
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returns
{ netowrk, view }
cyclient.network.show
cyclient.network.show(self, edgeList=None, network=None, nodeList=None, verbose=False)
Show nodes and/or edges in a network. A list of nodes and/or edges may be provided and those nodes and edges will be unhidden in the view associated with the provided network.Note that the network '''must''' have a view. The SUIDs of the unhidden nodes and/or edges are returned.
edgeList (string, optional)
Specifies a list of edges. The keywords all, selected, or unselected can be used to specify edges by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.nodeList (string, optional)
Specifies a list of nodes. The keywords all, selected, or unselected can be used to specify nodes by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.-
verbose
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returns
[ list of SUIDs of the unhidden nodes and/or edges ]
cyclient.network.add
cyclient.network.add(self, edgeList=None, network=None, nodeList=None, verbose=False)
Adds nodes and edges to an existing network. The nodes and edges to be added must already exist in the network collection. This command is most often used to populate a subnetwork with selected nodes and edges from a parent network.
edgeList
(string, optional), Specifies a list of edges. The keywords all, selected, or unselected can be used to specify edges by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.network
(string, optional), Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.nodeList
(string, optional), Specifies a list of nodes. The keywords all, selected, or unselected can be used to specify nodes by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.verbose
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cyclient.network.destroy
cyclient.network.destroy(self, network=None, verbose=False)
Destroy (delete) a network. The SUID of the destroyed network is returned.
network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.-
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returns
id of destroyed network
cyclient.network.load_file
cyclient.network.load_file(self, afile=None, verbose=False)
Load a new network from a network file type (e.g. SIF, XGMML, etc.). Use network import file to load networks from Excel or csv files. This command will create a new network collection if no current network collection is selected, otherwise it will add the network to the current collection. The SUIDs of the new networks and views are returned.
afile (string)
Select a network format file. This command does not support csv or Excel files. Use network import file for that.-
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returns
{ SUIDs of the new networks and views }
cyclient.network.set_current
cyclient.network.set_current(self, network=None, verbose=False)
Sets the current network, which can also be null. This will set the .network.network_name value to network.
network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.verbose
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cyclient.network.get
cyclient.network.get(self, network=None, verbose=False)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network. This function sets the self.network.network_name and self.network.network_suid of a cyclient object.
network: network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.-
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returns
{ dictionary with values for the respective network }
cyclient.network.clone
cyclient.network.clone(self, network=None, verbose=False)
Create a new network by cloning an existing network. The new network will be created as part of a new network collection. The SUID of the new network and view (if one is created) are returned.
name (string, optional)
The name of the node, which will be assigned to both the 'name' and 'shared name' columnsnetwork (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.-
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returns
{ network, view }
cyclient.network.get_attribute
cyclient.network.get_attribute(self, columnList=None, namespace=None, network=None, verbose=False)
Returns the attributes for the network passed as parameter.
columnList (string, optional)
A list of column names, separated by commas.namespace (string, optional)
Node, Edge, and Network objects support the default, local, and hidden namespaces. Root networks also support the shared namespace. Custom namespaces may be specified by Apps.network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.-
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returns
{ attributes for the network passed in column list }
cyclient.network.list_attributes
cyclient.network.list_attributes(self, namespace=None, network=None, verbose=False)
Returns a list of column names assocated with a network.
namespace (string, optional)
Node, Edge, and Network objects support the default, local, and hidden namespaces. Root networks also support the shared namespace. Custom namespaces may be specified by Apps.network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.-
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returns
[ list of column names assocated with a network ]
cyclient.network.create_attribute
cyclient.network.create_attribute(self, column=None, listType=None, namespace=None, network=None, atype=None, verbose=False)
Creates a new network column.
column (string, optional)
Unique name of columnlistType (string, optional)
Can be one of integer, long, double, or string. = ['integer', 'long', 'double', 'string', 'boolean']namespace (string, optional)
Node, Edge, and Network objects support the default, local, and hidden namespaces. Root networks also support the shared namespace. Custom namespaces may be specified by Apps.network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.atype (string, optional)
Can be one of integer, long, double, string, or list. = ['integer', 'long', 'double', 'string', 'boolean', 'list']-
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returns
{ columnName }
cyclient.network.add_edge
cyclient.network.add_edge(self, isDirected=None,name=None,network=None,sourceName=None,targetName=None, verbose=False)
Add a new edge between two existing nodes in a network. The names of the nodes must be specified and much match the value in the 'name' column for each node.
isDirected (string, optional)
Whether the edge should be directed or not. Even though all edges in Cytoscape have a source and target, by default they are treated as undirected. Setting this to 'true' will flag some algorithms to treat them as directed, although many current implementations will ignore this flag.name (string, optional)
Set the 'name' and 'shared name' columns for this edge to the provided value. ,network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.sourceName (string)
Enter the name of an existing node in the network to be the source of the edge. Note that this is the name as defined in the 'name' column of the network.targetName (string)
Enter the name of an existing node in the network to be the target of the edge. Note that this is the name as defined in the 'name' column of the network.verbose
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cyclient.network.create_empty
cyclient.network.create_empty(self, name=None, renderers=None, RootNetworkList=None, verbose=False)
Create a new, empty network. The new network may be created as part of an existing network collection or a new network collection.
name (string, optional)
Enter the name of the new network.renderers (string, optional)
Select the renderer to use for the new network view. By default, the standard Cytoscape 2D renderer (Ding) will be used = [''],RootNetworkList (string, optional)
Choose the network collection the new network should be part of. If no network collection is selected, a new network collection is created. = [' -- Create new network collection --', 'cy:command_documentation_generation']verbose
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cyclient.network.import_file
cyclient.network.import_file(self, dataTypeList=None, defaultInteraction=None, delimiters=None, delimitersForDataList=None, afile=None, firstRowAsColumnNames=None, \ indexColumnSourceInteraction=None, indexColumnTargetInteraction=None, indexColumnTypeInteraction=None, \ NetworkViewRendererList=None, RootNetworkList=None, startLoadRow=None,\ TargetColumnList=None, verbose=False)
Import a new network from a tabular formatted file type (e.g. csv, tsv, Excel, etc.). Use network load file to load network formatted files. This command will create a new network collection if no current network collection is selected, otherwise it will add the network to the current collection. The SUIDs of the new networks and views are returned.
dataTypeList (string, optional)
List of column data types ordered by column index (e.g. "string,int,long,double,boolean,intlist" or just "s,i,l,d,b,il"): ,defaultInteraction (string, optional)
Used to set the default interaction type to use when there is no interaction type column.delimiters (string, optional)
Select the delimiters to use to separate columns in the table, from the list ',',' ','TAB', or ';'. TAB and ',' are used by default = [',', ';', ' ', '\t']delimitersForDataList (string, optional)
Select the delimiters to use to separate list entries in a list, from the list '|','\','/', or ','. | is used by default = ['|', '\', '/', ',']afile (string)
The path to the file that contains the table or network to be imported.firstRowAsColumnNames (string, optional)
If this is true then the first row should contain the names of the columns. Note that startLoadRow must be set for this to work properlyindexColumnSourceInteraction (string)
The column index that contains the source node identifiers.indexColumnTargetInteraction (string, optional)
The column index that contains the target node identifiers. If this is not specified then the resulting network will have no edgesindexColumnTypeInteraction (string, optional)
The column index that contains the interaction type. This is not required.NetworkViewRendererList (string, optional)
Enter the network view renderer that this network should use. This is only useful if multiple renderers have been installed, which is rare. = ['']RootNetworkList (string, optional)
The name of the network collection (root network) that the imported network should be part of. A name of -- Create new network collection -- will result in the creation of a new network collection for this import. = ['-- Create new network collection --', 'cy:command_documentation_generation']startLoadRow (string, optional)
The starting row of the import. This is used to skip over comments and other non-data rows at the beginning of the file.TargetColumnList (string, optional)
Enter the name of the column in the existing network collection (root network) that you want to map your input identifiers to. = ['']-
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returns
{ SUIDs of the new networks and views }
cyclient.network.list
cyclient.network.list(self, verbose=False)
List all of the networks in the current session.
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verbose
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returns
[ list of network suids ]
cyclient.network.set_attribute
cyclient.network.set_attribute(self, columnList=None, namespace=None, network=None, valueList=None, verbose=False)
Set a value in the network table.
columnList (string, optional)
A list of column names, separated by commas.namespace (string, optional)
Node, Edge, and Network objects support the default, local, and hidden namespaces. Root networks also support the shared namespace. Custom namespaces may be specified by Apps.network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.valueList (string, optional)
A list of values, separated by commas. List values can be included using the format [value1,value2].verbose
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cyclient.network.set_properties
cyclient.network.set_properties(self, network=None, propertyList=None, valueList=None, verbose=False)
Set network visual properties.
network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.propertyList (string)
A comma-separated list of network propertiesvalueList (string)
A comma-separated list of property values. This list must have the same number of elements as the propertyList. Each value will be applied to the property specified in the same position in the propertyListverbose
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cyclient.network.connect_nodes
cyclient.network.connect_nodes(self, network=None, nodes=None, verbose=False)
Create new edges that connect a list of nodes.
network (string)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.nodes (string)
Specifies a list of nodes. The keywords all, selected, or unselected can be used to specify nodes by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.-
verbose
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returns
[ list of generated edges ]
cyclient.network.delete
cyclient.network.delete(self, edgeList=None, network=None, nodeList=None, verbose=False)
Deletes nodes and edges provided by the arguments, or if no nodes or edges are provides, the selected nodes and edges. When deleting nodes, adjacent edges are also deleted.
edgeList (string, optional)
Specifies a list of edges. The keywords all, selected, or unselected can be used to specify edges by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.network (string, optional)
Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.nodeList (string, optional)
Specifies a list of nodes. The keywords all, selected, or unselected can be used to specify nodes by their selection state. The pattern COLUMN:VALUE sets this parameter to any rows that contain the specified column value; if the COLUMN prefix is not used, the NAME column is matched by default. A list of COLUMN:VALUE pairs of the format COLUMN1:VALUE1,COLUMN2:VALUE2,... can be used to match multiple values.verbose
print more