NetworkX static and dynamic visualizations (pyvipr.networkx_viz.network_viz)

NetworkX visualization views (pyvipr.networkx_viz.views)

pyvipr.network_viz.views.nx_graph_view(graph, layout_name='cose')[source]

Render a networkx Graph or DiGraph :param graph: Graph to render :type graph: nx.Graph or nx.DiGraph :param layout_name: Layout to use :type layout_name: str

pyvipr.network_viz.views.nx_graph_dyn_view(graph, tspan, node_rel=None, node_tip=None, edge_colors=None, edge_sizes=None, edge_tips=None, layout_name='cose')[source]

Render a dynamic visualization of a networkx graph

Parameters

  • graph (nx.DiGraph or nx.Graph) – Graph to visualize

  • tspan (vector-like, optional) – Time values over which to simulate. The first and last values define

  • node_rel (dict) – A dictionary where the keys are the node ids and the values are lists that contain (0-100) values that are represented in a pie chart within the node

  • node_tip (dict) – A dictionary where the keys are the node ids and the values are lists that contain any value that can be accessed as a tooltip in the rendered network

  • edge_colors (dict) – A dictionary where the keys are the edge ids and the values are lists that contain any hexadecimal color value that are represented in the edge colors

  • edge_sizes (dict) – A dictionary where the keys are the edge ids and the values are lists that contain any numerical value that are represented in the edge size

  • edge_tips (dict) – A dictionary where the keys are the edge ids and the values are lists that contain any value that can be accessed as a tooltip in the rendered network

  • layout_name (str) – Layout to use

pyvipr.network_viz.views.graphml_view(file, layout_name='fcose')[source]

Read graph stored in GRAPHML format using NetworkX and render a visualization of it

Parameters

  • file (str) – Path to file in graphml format

  • layout_name (str) – Name of layout to use

pyvipr.network_viz.views.sif_view(file, layout_name='fcose')[source]

Read graph stored in SIF format using NetworkX and render a visualization of it

Parameters

  • file (str) – Path to file in sif format

  • layout_name (str) – Name of layout to use

pyvipr.network_viz.views.sbgn_xml_view(file, layout_name='fcose')[source]

Read graph stored in SBGN XML format using NetworkX and render a visualization of it

Parameters

  • file (str) – Path to file in SBGN XML format

  • layout_name (str) – Name of layout to use

pyvipr.network_viz.views.json_view(file, layout_name='fcose')[source]

Read graph stored in cytoscape json format using NetworkX and render a visualization of it

Parameters

  • file (str) – Path to file in cytoscape json format

  • layout_name (str) – Name of layout to use

pyvipr.network_viz.views.dynamic_json_view(file, layout_name='fcose')[source]

Read graph stored in cytoscape json format using NetworkX and render a visualization of it. This function is for graphs saved from dynamic visualizations.

Parameters

  • file (str) – Path to file in cytoscape json format

  • layout_name (str) – Name of layout to use

pyvipr.network_viz.views.gexf_view(file, node_type=None, relabel=False, version='1.2draft', layout_name='fcose')[source]

Read graph stored in GEXF format using NetworkX and render a visualization of it

Parameters

  • file (str) – Path to file in gexf format

  • node_type (Python type (default: none)) – Convert node ids to this type if not None

  • relabel (bool (default: False)) – If True relabel the nodes to use the GEXF node “label attribute” instead of the node “id” attribute as the NetworkX node label

  • version (str (default: 1.2draft)) – Version of GEFX File Format (see https://gephi.org/gexf/format/schema.html). Supported values: “1.1draft”, “1.2dra

  • layout_name (str) – Name of layout to use

pyvipr.network_viz.views.gml_view(file, label='label', destringizer=None, layout_name='fcose')[source]

Read graph stored in GML format using NetworkX and render a visualization of it

Parameters

  • file (str) – Path to file in cytoscape json format

  • label (str, optional) – If not None, the pased nodes will be renamed according to node attributes indicated by label. Default value: ‘label’

  • destringizer (callable, optional) – A destringizer that recovers values stored as strings in GML. If it cannot convert a string to a value, a ValueError is raised. Default value: None

  • layout_name (str) – Name of layout to use

pyvipr.network_viz.views.yaml_view(file, layout_name='fcose')[source]

Read graph stored in YAML format using NetworkX and render a visualization of it

Parameters

  • file (str) – Path to file in YAML format

  • layout_name (str) – Name of layout to use