NiceCXNetwork¶

The NiceCXNetwork class provides a data model for working with NDEx networks that are stored in CX format

Note

The term niceCX is CX with no duplicate aspects.

Methods are provided to add nodes, edges, node attributes, edge attributes, etc. Once a NiceCXNetwork object is populated it can be saved to the NDEx server by calling either upload_to() to create a new network or upload_to() to update an existing network.

Methods¶

Example usage of the methods below can be found in the Jupyter notebook links here:

Tutorial Notebook Navigating NiceCXNetwork Notebook

Node methods¶

class ndex2.nice_cx_network.NiceCXNetwork(**attr)[source]¶

create_node(node_name=None, node_represents=None)[source]¶

Creates a new node with the corresponding name and represents (external id)

Example:

my_node = create_node(node_name='MAPK1, node_represents='1114208')

Parameters:	node_name (str) – Name of the node node_represents (str) – Representation of the node (alternate identifier)
Returns:	Node ID
Return type:	int

get_node_attribute(node, attribute_name)[source]¶

Get the node attribute of a node, where the node may be specified by its id or passed in as an object.

Example:

get_node_attribute(my_node, 'Pathway') # returns: {'@id': 0, 'n': 'diffusion-heat', 'v': 0.832, 'd': 'double'}

Parameters:	node (int or node dict with @id attribute) – node object or node id attribute_name – attribute name
Returns:	the node attibute object or None if the attribute doesn’t exist
Return type:	dict

get_node_attribute_value(node, attribute_name)[source]¶

Get the value(s) of an attribute of a node, where the node may be specified by its id or passed in as an object.

Example:

get_node_attribute_value(my_node, 'Pathway') # returns: 'Signal Transduction / Growth Regulation'

Parameters:	node (int or node dict with @id attribute) – node object or node id attribute_name – attribute name
Returns:	the value of the attibute or None if the attribute doesn’t exist
Return type:	string

get_node_attributes(node)[source]¶

Get the attribute objects of a node, where the node may be specified by its id or passed in as an object.

Example:

get_node_attributes(my_node) # returns: [{'po': 0, 'n': 'Pathway', 'v': 'Signal Transduction / Growth Regulation'}]

Parameters:	node (int or node dict with @id attribute) – node object or node id
Returns:	node attributes
Return type:	list

get_nodes()[source]¶

Returns an iterator over node ids as keys and node objects as values.

Example:

for id, node in nice_cx.get_nodes():

node_name = node.get('n')

node_represents = node.get('r')

Returns:	iterator over nodes
Return type:	iterator

set_node_attribute(node, attribute_name, values, type=None, overwrite=False)[source]¶

Set an attribute of a node, where the node may be specified by its id or passed in as a node dict.

Example:

set_node_attribute(my_node, 'Pathway', 'Signal Transduction / Growth Regulation')

or

set_node_attribute(my_node, 'Mutation Frequency', 0.007, type='double')

Parameters:	node (int or node dict with @id attribute) – Node to add the attribute to attribute_name (string) – attribute name values (list, string, int or double) – A value or list of values of the attribute type (str) – The datatype of the attribute values, defaults is string. See Supported data types overwrite (bool True means to overwrite node attribute named attribute_name) – If True node attribute matching ‘attribute_name’ is removed first otherwise code blindly adds attribute
Returns:	None
Return type:	None

Edge methods¶

class ndex2.nice_cx_network.NiceCXNetwork(**attr)[source]

create_edge(edge_source=None, edge_target=None, edge_interaction=None)[source]¶

Create a new edge in the network by specifying source-interaction-target

Example:

my_edge = create_edge(edge_source=my_node, edge_target=my_node2, edge_interaction='up-regulates')

Parameters:	edge_source (int, dict (with `EDGE_ID` property)) – The source node of this edge, either its id or the node object itself. edge_target (int, dict (with `EDGE_ID` property)) – The target node of this edge, either its id or the node object itself. edge_interaction (string) – The interaction that describes the relationship between the source and target nodes
Returns:	Edge ID
Return type:	int

get_edge_attribute(edge, attribute_name)[source]¶

Get the edge attributes of an edge, where the edge may be specified by its id or passed in as an object.

Example:

get_edge_attribute(my_edge, 'weight')

# returns: {'@id': 0, 'n': 'weight', 'v': 0.849, 'd': 'double'}

Parameters:	edge (int or edge dict with @id attribute) – Edge object or edge id attribute_name – Attribute name
Returns:	Edge attribute object
Return type:	list, string, int or double

get_edge_attribute_value(edge, attribute_name)[source]¶

Get the value(s) of an attribute of an edge, where the edge may be specified by its id or passed in as an object.

Example:

get_edge_attribute_value(my_edge, 'weight')

# returns: 0.849

Parameters:	edge (int or edge dict with @id attribute) – Edge object or edge id attribute_name – Attribute name
Returns:	Edge attribute value(s)
Return type:	list, string, int or double

get_edge_attributes(edge)[source]¶

Get the attribute objects of an edge, where the edge may be specified by its id or passed in as an object.

Example:

get_edge_attributes(my_edge)

# returns: [{'@id': 0, 'n': 'weight', 'v': 0.849, 'd': 'double'}, {'@id': 0, 'n': 'Type', 'v': 'E1'}]

Parameters:	edge (int or edge dict with @id attribute) – Edge object or edge id
Returns:	Edge attribute objects
Return type:	list of edge dict

get_edges()[source]¶

Returns an iterator over edge ids as keys and edge objects as values.

Example:

for edge_id, edge_obj in nice_cx.get_edges():

print(edge_obj.get('i')) # print interaction

print(edge_obj.get('s')) # print source node id

Returns:	Edge iterator
Return type:	iterator

set_edge_attribute(edge, attribute_name, values, type=None)[source]¶

Set the value(s) of attribute of an edge, where the edge may be specified by its id or passed in an object.

Example:

set_edge_attribute(0, 'weight', 0.5, type='double')

or

set_edge_attribute(my_edge, 'Disease', 'Atherosclerosis')

Parameters:	edge (int or edge dict with @id attribute) – Edge to add the attribute to attribute_name (str) – Attribute name values (list) – A value or list of values of the attribute type (str) – The datatype of the attribute values, defaults to the python datatype of the values. See Supported data types
Returns:	None
Return type:	None

Network methods¶

class ndex2.nice_cx_network.NiceCXNetwork(**attr)[source]

get_context()[source]¶

Get the @context information of the network. This information maps namespace prefixes to their defining URIs

Example:

{'pmid': 'https://www.ncbi.nlm.nih.gov/pubmed/'}

Returns:	context object
Return type:	dict

get_name()[source]¶

Get the network name

Returns:	Network name
Return type:	string

get_network_attribute(attribute_name)[source]¶

Get the value of a network attribute

Parameters:	attribute_name (string) – Attribute name
Returns:	Network attribute object
Return type:	dict

get_network_attribute_names()[source]¶

Creates a a generator that gets network attribute names.

Returns:	attribute name via a generator
Return type:	string

get_opaque_aspect(aspect_name)[source]¶

Get the elements of the aspect specified by aspect_name

Parameters:	aspect_name (string) – the name of the aspect to retrieve.
Returns:	Opaque aspect
Return type:	list of aspect elements

set_context(context)[source]¶

Set the @context information of the network. This information maps namespace prefixes to their defining URIs

Example:

set_context({'pmid': 'https://www.ncbi.nlm.nih.gov/pubmed/'})

Parameters:	context (dict) – dict of name, URI pairs
Returns:	None
Return type:	none

set_name(network_name)[source]¶

Set the network name

Example:

set_name('P38 Signaling')

Parameters:	network_name (string) – Network name
Returns:	None
Return type:	None

set_network_attribute(name, values=None, type=None)[source]¶

Set an attribute of the network

Example:

set_network_attribute(name='networkType', values='Genetic interactions')

Parameters:	name (string) – Attribute name values (list, string, double or int) – The values of the attribute type (str) – The datatype of the attribute values. See Supported data types
Returns:	None
Return type:	none

set_opaque_aspect(aspect_name, aspect_elements)[source]¶

Set the aspect specified by aspect_name to the list of aspect elements. If aspect_elements is None, the aspect is removed.

Parameters:	aspect_name (string) – Name of the aspect aspect_elements (list of dict) – Aspect element
Returns:	None
Return type:	none

Miscellaneous methods¶

class ndex2.nice_cx_network.NiceCXNetwork(**attr)[source]

apply_style_from_network(nicecxnetwork)[source]¶

Applies Cytoscape visual properties from the network passed into this method. The style is pulled from VISUAL_PROPERTIES or CY_VISUAL_PROPERTIES

Parameters:	nicecxnetwork (`NiceCXNetwork`) – Network to extract style from
Raises:	TypeError – If object passed in is NOT a `NiceCXNetwork` object or if object is None NDExError – If `NiceCXNetwork` does not have any visual styles
Returns:	None
Return type:	None

apply_template(server, uuid, username=None, password=None)[source]¶

Applies the Cytoscape visual properties of a network from the provideduuid to this network.

This allows the use of networks formatted in Cytoscape as templates to apply visual styles to other networks.

Example:

nice_cx.apply_template('public.ndexbio.org', '51247435-1e5f-11e8-b939-0ac135e8bacf')

Parameters:	server (string) – server host name (i.e. public.ndexbio.org) username (string) – username (optional - used when accessing private networks) password (string) – password (optional - used when accessing private networks) uuid (string) – uuid of the styled network
Returns:	None
Return type:	None

print_summary()[source]¶

Print a network summary

Returns:	Network summary
Return type:	string

to_cx()[source]¶

Return the CX corresponding to the network.

Returns:	CX representation of the network
Return type:	CX (list of dict aspects)

to_cx_stream()[source]¶

Returns a stream of the CX corresponding to the network. Can be used to post to endpoints that can accept streaming inputs

Returns:	The CX stream representation of this network.
Return type:	io.BytesIO

to_networkx(mode='legacy')[source]¶

Returns a NetworkX Graph() object or one of its subclasses based on the network. The mode parameter dictates how the translation occurs.

This method currently supports the following mode values:

Warning

For backwards compatibility mode is set to legacy but there are known bugs in this implementation when networkx 2.0+ or greater is installed.

See the description on legacy mode below for more information.

Modes:

legacy:

If mode set to legacy then this method will behave as it has for all versions of NDEx2 Python Client 3.1.0 and earlier which varies depending on version of networkx installed as described here:

For networkx 2.0 and greater: (see LegacyNetworkXVersionTwoPlusFactory)

For older versions of networkx the following class is used with the legacymode parameter set to True: (see DefaultNetworkXFactory)

default:

If mode is default or None then this method uses DefaultNetworkXFactory regardless of networkx installed with legacymode set to False

Note

default mode is the preferred mode to use

Examples:

# returns networkx graph using improved converter
graph = nice_cx.to_networkx(mode='default')

# returns networkx graph using legacy implementation
graph = nice_cx.to_networkx()

# returns networkx graph using legacy implementation
graph = nice_cx.to_networkx()

Parameters:	mode (string) – Since translation to networkx can be done in many ways this mode lets the caller dictate the method.
Raises:	NDExError – If mode is not None, ‘legacy’, or ‘default’
Returns:	Networkx graph
Return type:	`networkx.Graph` or `networkx.MultiGraph`

to_pandas_dataframe()[source]¶

Export the network as a Pandas DataFrame.

Example:

df = nice_cx.to_pandas_dataframe() # df is now a pandas dataframe

Note: This method only processes nodes, edges, node attributes and edge attributes, but not network attributes or other aspects

Returns:	Pandas dataframe
Return type:	Pandas dataframe

update_to(uuid, server, username, password, user_agent='')[source]¶

Upload this network to the specified server to the account specified: by username and password.

Example:

nice_cx.update_to('2ec87c51-c349-11e8-90ac-525400c25d22', 'public.ndexbio.org', username, password)

Parameters:	server (str) – The NDEx server to upload the network to. username (str) – The username of the account to store the network. password (str) – The password for the account. user_agent (string) – String to append to User-Agent field sent to NDEx REST service
Returns:	The UUID of the network on NDEx.
Return type:	str

upload_to(server, username, password, user_agent='')[source]¶

Upload this network to the specified server to the account specified: by username and password.

Example:

nice_cx.upload_to('http://public.ndexbio.org', username, password)

Parameters:	server (string) – The NDEx server to upload the network to. username (string) – The username of the account to store the network. password (string) – The password for the account. user_agent (string) – String to append to User-Agent field sent to NDEx REST service
Returns:	The UUID of the network on NDEx.
Return type:	string

Supported data types¶

The following data types are supported in methods that accept type

Example:

set_edge_attribute(0, 'weight', 0.5, type='double')

string
double
boolean
integer
long
list_of_string
list_of_double
list_of_boolean
list_of_integer
list_of_long

These constants are defined here: VALID_ATTRIBUTE_DATATYPES