CytoViewer#

class biopax-explorer.graph.view.CytoViewer(graph, gtype='NX')[source]#

Bases: object

A wrapper for the cytoscape.js jupyter widget.

Methods

`addStyle`(cstyle)	Adds additional style to the final style settings.
`defineEdgeLabel`([attlist, separator, attName])	Defines the label attribute for edges.
`defineEdgeLabelImpl`()	Defines the label attribute for edges based on defined attributes and separator.
`defineNodeLabel`([attlist, separator, attName])	Defines the label attribute for nodes.
`defineNodeLabelImpl`()	Defines the label attribute for nodes based on defined attributes and separator.
`defineShapes`()	Defines the possible shapes for node representation.
`defineViewer`()	Defines the viewer for displaying the graph.
`define_default_style`(nodeLabel, edgeLabel)	Defines the default style settings for nodes and edges.
`display`([nodeLabel, edgeLabel])	Displays the graph with specified node and edge labels.
`from_graphtool`(g)	Converts a graph-tool graph to a CytoViewer graph.
`from_json`(data)	Loads graph data from JSON format.
`from_networkx`(g)	Converts a NetworkX graph to a CytoViewer graph.
`generate_node_selector`()	Generates node selector styles based on defined color schemes.
`generate_web_colors`(start_color, end_color, ...)	Generates a list of web colors between two specified colors.
`initStyle`(nodeLabel, edgeLabel)	Initializes the style settings for the graph nodes and edges.
`initViewFromGraph`()	Initializes the viewer from the provided graph.
`layout`(layoutname)	Sets the layout for graph visualization.
`nodeSelector`(attribute_key, attribute_value)	Selects nodes in the graph based on the specified attribute key and value, and applies a custom style to them.
`select_list_alternatively`(a, b, c, d, e, x)	Selects a list from the provided lists alternately based on the value of x.
`style`(cstyle)	Sets the final style settings.
`tooltip`(tooltip)	Sets the tooltip source for graph elements.

gf2nx

Methods Summary

`addStyle`(cstyle)	Adds additional style to the final style settings.
`defineEdgeLabel`([attlist, separator, attName])	Defines the label attribute for edges.
`defineEdgeLabelImpl`()	Defines the label attribute for edges based on defined attributes and separator.
`defineNodeLabel`([attlist, separator, attName])	Defines the label attribute for nodes.
`defineNodeLabelImpl`()	Defines the label attribute for nodes based on defined attributes and separator.
`defineShapes`()	Defines the possible shapes for node representation.
`defineViewer`()	Defines the viewer for displaying the graph.
`define_default_style`(nodeLabel, edgeLabel)	Defines the default style settings for nodes and edges.
`display`([nodeLabel, edgeLabel])	Displays the graph with specified node and edge labels.
`from_graphtool`(g)	Converts a graph-tool graph to a CytoViewer graph.
`from_json`(data)	Loads graph data from JSON format.
`from_networkx`(g)	Converts a NetworkX graph to a CytoViewer graph.
`generate_node_selector`()	Generates node selector styles based on defined color schemes.
`generate_web_colors`(start_color, end_color, ...)	Generates a list of web colors between two specified colors.
`gf2nx`(g)
`initStyle`(nodeLabel, edgeLabel)	Initializes the style settings for the graph nodes and edges.
`initViewFromGraph`()	Initializes the viewer from the provided graph.
`layout`(layoutname)	Sets the layout for graph visualization.
`nodeSelector`(attribute_key, attribute_value)	Selects nodes in the graph based on the specified attribute key and value, and applies a custom style to them.
`select_list_alternatively`(a, b, c, d, e, x)	Selects a list from the provided lists alternately based on the value of x.
`style`(cstyle)	Sets the final style settings.
`tooltip`(tooltip)	Sets the tooltip source for graph elements.

Methods Documentation

addStyle(cstyle)[source]#

Adds additional style to the final style settings.

Args:: cstyle (list): List of dictionaries representing additional style settings.
Returns:: None

defineEdgeLabel(attlist=['name'], separator=' ', attName='elabel')[source]#

Defines the label attribute for edges.

Args:: attlist (list): List of edge attributes to include in the label. separator (str): Separator to use between attribute values. attName (str): Name of the label attribute.
Returns:: None

defineEdgeLabelImpl()[source]#

Defines the label attribute for edges based on defined attributes and separator.

Returns:: None

defineNodeLabel(attlist=['name'], separator=' ', attName='nlabel')[source]#

Defines the label attribute for nodes.

Args:: attlist (list): List of node attributes to include in the label. separator (str): Separator to use between attribute values. attName (str): Name of the label attribute.
Returns:: None

defineNodeLabelImpl()[source]#

Defines the label attribute for nodes based on defined attributes and separator.

Returns:: None

defineShapes()[source]#

Defines the possible shapes for node representation.

Returns:: list: List of strings representing node shapes.

defineViewer()[source]#

Defines the viewer for displaying the graph.

Returns:: cyto.CytoscapeWidget: The cytoscape.js widget for graph visualization.

define_default_style(nodeLabel, edgeLabel)[source]#

Defines the default style settings for nodes and edges.

Args:: nodeLabel (str): The label attribute for nodes. edgeLabel (str): The label attribute for edges.
Returns:: list: List of dictionaries representing default style settings.

display(nodeLabel='nlabel', edgeLabel='elabel')[source]#

Displays the graph with specified node and edge labels.

Args:: nodeLabel (str): Label attribute for nodes. edgeLabel (str): Label attribute for edges.
Returns:: cyto.CytoscapeWidget: The cytoscape.js widget displaying the graph.

from_graphtool(g)[source]#

Converts a graph-tool graph to a CytoViewer graph.

Args:: graph (Graph): The input graph-tool graph.
Returns:: cyto.CytoscapeWidget: The CytoViewer graph.

from_json(data)[source]#

Loads graph data from JSON format.

Args:: data (str): JSON data representing the graph.
Returns:: None

from_networkx(g)[source]#

Converts a NetworkX graph to a CytoViewer graph.

Args:: graph (nx.Graph): The input NetworkX graph.
Returns:: cyto.CytoscapeWidget: The CytoViewer graph.

generate_node_selector()[source]#

Generates node selector styles based on defined color schemes.

Returns:: list: List of dictionaries representing node selector styles.

generate_web_colors(start_color, end_color, num_colors)[source]#

Generates a list of web colors between two specified colors.

Args:: start_color (str): The starting color. end_color (str): The ending color. steps (int): The number of steps.
Returns:: List[str]: A list of web colors.

gf2nx(g)[source]#

initStyle(nodeLabel, edgeLabel)[source]#

Initializes the style settings for the graph nodes and edges.

Args:: nodeLabel (str): The label attribute for nodes. edgeLabel (str): The label attribute for edges.

initViewFromGraph()[source]#: Initializes the viewer from the provided graph.

layout(layoutname)[source]#

Sets the layout for graph visualization.

Args:: layoutname (str): Name of the layout.
Returns:: None

nodeSelector(attribute_key, attribute_value, operator='IN', color='red')[source]#

Selects nodes in the graph based on the specified attribute key and value, and applies a custom style to them.

Args:

attribute_key (str): The key of the attribute to filter nodes by. attribute_value (str): The value of the attribute to filter nodes by. operator (str, optional): The comparison operator to use for filtering.

Defaults to “IN”. Can be “IN” for “inclusion” or “EQ” for “equality”.

color (str, optional): The color to apply to the selected nodes. Defaults to “red”.

Returns:

list: A list of custom styles applied to the selected nodes.

select_list_alternatively(a, b, c, d, e, x)[source]#

Selects a list from the provided lists alternately based on the value of x.

Args:: a, b, c, d, e (list): Lists to select from. x (int): Value used for selection.
Returns:: list: The selected list.

style(cstyle)[source]#

Sets the final style settings.

Args:: cstyle (list): List of dictionaries representing final style settings.
Returns:: None

tooltip(tooltip)[source]#

Sets the tooltip source for graph elements.

Args:: tooltip (str): Tooltip source.
Returns:: None