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biograph object - Data structure containing generic interconnected data used to implement directed graph

Description

A biograph object is a data structure containing generic interconnected data used to implement a directed graph. Nodes represent proteins, genes, or any other biological entity, and edges represent interactions, dependences, or any other relationship between the nodes. A biograph object also stores information, such as color properties and text label characteristics, used to create a 2-D visualization of the graph.

You create a biograph object using the object constructor function biograph. You can view a graphical representation of a biograph object using the view method.

Method Summary

Following are methods of a biograph object:

allshortestpaths (biograph)	Find all shortest paths in biograph object
conncomp (biograph)	Find strongly or weakly connected components in biograph object
dolayout (biograph)	Calculate node positions and edge trajectories
get (biograph)	Retrieve information about biograph object
getancestors (biograph)	Find ancestors in biograph object
getdescendants (biograph)	Find descendants in biograph object
getedgesbynodeid (biograph)	Get handles to edges in biograph object
getmatrix (biograph)	Get connection matrix from biograph object
getnodesbyid (biograph)	Get handles to nodes
getrelatives (biograph)	Find relatives in biograph object
isdag (biograph)	Test for cycles in biograph object
isomorphism (biograph)	Find isomorphism between two biograph objects
isspantree (biograph)	Determine if tree created from biograph object is spanning tree
maxflow (biograph)	Calculate maximum flow in biograph object
minspantree (biograph)	Find minimal spanning tree in biograph object
set (biograph)	Set property of biograph object
shortestpath (biograph)	Solve shortest path problem in biograph object
topoorder (biograph)	Perform topological sort of directed acyclic graph extracted from biograph object
traverse (biograph)	Traverse biograph object by following adjacent nodes
view (biograph)	Draw figure from biograph object

Following are methods of a node object:

getancestors (biograph)	Find ancestors in biograph object
getdescendants (biograph)	Find descendants in biograph object
getrelatives (biograph)	Find relatives in biograph object

Property Summary

A biograph object contains two kinds of objects, node objects and edge objects, that have their own properties. For a list of the properties of node objects and edge objects, see the following tables.

Properties of a Biograph Object

Property	Description
ID	String to identify the biograph object. Default is ''.
Label	String to label the biograph object. Default is ''.
Description	String that describes the biograph object. Default is ''.
LayoutType	String that specifies the algorithm for the layout engine. Choices are: 'hierarchical' (default) — Uses a topological order of the graph to assign levels, and then arranges the nodes from top to bottom, while minimizing crossing edges. 'radial' — Uses a topological order of the graph to assign levels, and then arranges the nodes from inside to outside of the circle, while minimizing crossing edges. 'equilibrium' — Calculates layout by minimizing the energy in a dynamic spring system.
EdgeType	String that specifies how edges display. Choices are: 'straight' 'curved' (default) 'segmented' Note   Curved or segmented edges occur only when necessary to avoid obstruction by nodes. Biograph objects with LayoutType equal to 'equilibrium' or 'radial' cannot produce curved or segmented edges.
Scale	Positive number that post-scales the node coordinates. Default is 1.
LayoutScale	Positive number that scales the size of the nodes before calling the layout engine. Default is 1.
EdgeTextColor	Three-element numeric vector of RGB values. Default is [0, 0, 0], which defines black.
EdgeFontSize	Positive number that sets the size of the edge font in points. Default is 8.
ShowArrows	Controls the display of arrows with the edges. Choices are 'on' (default) or 'off'.
ArrowSize	Positive number that sets the size of the arrows in points. Default is 8.
ShowWeights	Controls the display of text indicating the weight of the edges. Choices are 'on' (default) or 'off'.
ShowTextInNodes	String that specifies the node property used to label nodes when you display a biograph object using the view method. Choices are: 'Label' — Uses the Label property of the node object (default). 'ID' — Uses the ID property of the node object. 'None'
NodeAutoSize	Controls precalculating the node size before calling the layout engine. Choices are 'on' (default) or 'off'.
NodeCallback	User-defined callback for all nodes. Enter the name of a function, a function handle, or a cell array with multiple function handles. After using the view function to display the biograph object in the Biograph Viewer, you can double-click a node to activate the first callback, or right-click and select a callback to activate. Default is the anonymous function, @(node) inspect(node), which displays the Property Inspector dialog box.
EdgeCallback	User-defined callback for all edges. Enter the name of a function, a function handle, or a cell array with multiple function handles. After using the view function to display the biograph object in the Biograph Viewer, you can double-click an edge to activate the first callback, or right-click and select a callback to activate. Default is the anonymous function, @(edge) inspect(edge), which displays the Property Inspector dialog box.
CustomNodeDrawFcn	Function handle to a customized function to draw nodes. Default is [].
Nodes	Read-only column vector with handles to node objects of a biograph object. The size of the vector is the number of nodes. For properties of node objects, see Properties of a Node Object.
Edges	Read-only column vector with handles to edge objects of a biograph object. The size of the vector is the number of edges. For properties of edge objects, see Properties of an Edge Object.

Properties of a Node Object

Property	Description
ID	Character string defined when the biograph object is created, either by the NodeIDs input argument or internally by the biograph constructor function. You can modify this property using the set method, but each node object's ID must be unique.
Label	String for labeling a node when you display a biograph object using the view method. Default is ''.
Description	String that describes the node. Default is ''.
Position	Two-element numeric vector of x- and y-coordinates, for example, [150, 150]. If you do not specify this property, default is initially [], then when the layout algorithms are executed, it becomes a two-element numeric vector of x- and y-coordinates computed by the layout engine.
Shape	String that specifies the shape of the nodes. Choices are: 'box'(default) 'ellipse' 'circle' 'rectangle' 'diamond' 'trapezium' 'invtrapezium' 'house' 'inverse' 'parallelogram'
Size	Two-element numeric vector calculated before calling the layout engine using the actual font size and shape of the node. Default is [10, 10].
Color	Three-element numeric vector of RGB values that specifies the fill color of the node. Default is [1, 1, 0.7], which defines yellow.
LineWidth	Positive number. Default is 1.
LineColor	Three-element numeric vector of RGB values that specifies the outline color of the node. Default is [0.3, 0.3, 1], which defines blue.
FontSize	Positive number that sets the size of the node font in points. Default is 8.
TextColor	Three-element numeric vector of RGB values that specifies the color of the node labels. Default is [0, 0, 0], which defines black.
UserData	Miscellaneous, user-defined data that you want to associate with the node. The node does not use this property, but you can access and specify it using the get and set functions. Default is [].

Properties of an Edge Object

Property	Description
ID	Character string automatically generated from the node IDs when the biograph object is created by the biograph constructor function. You can modify this property using the set method, but each edge object's ID must be unique.
Label	String for labeling an edge when you display a biograph object using the view method. Default is ''.
Description	String that describes the edge. Default is ''.
Weight	Value that represents the weight (cost, distance, length, or capacity) associated with the edge. Default is 1.
LineWidth	Positive number. Default is 1.
LineColor	Three-element numeric vector of RGB values that specifies the color of the edge. Default is [0.5, 0.5, 0.5], which defines gray.
UserData	Miscellaneous, user-defined data that you want to associate with the edge. The edge does not use this property, but you can access and specify it using the get and set functions. Default is [].

Examples

Determining Properties and Property Values of a Biograph Object

You can display all properties and their current values of a biograph object, BGobj, by using the following syntax:

get(BGobj)

You can return all properties and their current values of BGobj, a biograph object, to BGstruct, a scalar structure in which each field name is a property of a biograph object, and each field contains the value of that property, by using the following syntax:

BGstruct = get(BGobj)

You can return the value of a specific property of a biograph object, BGobj, by using either of the following syntaxes:

PropertyValue = get(BGobj, 'PropertyName')

PropertyValue = BGobj.PropertyName

You can return the value of specific properties of a biograph object, BGobj, by using the following syntax:

[Property1Value, Property2Value, ...] = get(BGobj, ...
 'Property1Name', 'Property2Name', ...)

Determining Properties and Property Values of a Node or Edge of a Biograph Object

You can display all properties and their current values of the nth node or nth edge of a biograph object, BGobj, by using the following syntaxes:

get(BGobj.nodes(n))

get(BGobj.edges(n))

Determining Possible Values of Biograph Object Properties

You can display possible values for all properties that have a fixed set of property values in a biograph object, BGobj, by using the following syntax:

set(BGobj)

You can display possible values for a specific property that has a fixed set of property values in a biograph object, BGobj, by using the following syntax:

set(BGobj,  'PropertyName')

Specifying Properties of a Biograph Object

You can set a specific property of a biograph object, BGobj, by using either of the following syntaxes:

set(BGobj, 'PropertyName', PropertyValue)

BGobj.PropertyName = PropertyValue

You can set multiple properties of a biograph object, BGobj, by using the following syntax:

set(BGobj,  'Property1Name', Property1Value, ...
'Property2Name', Property2Value, ...)

Specifying Properties of a Node of a Biograph Object

You can set a specific property of the nth node of a biograph object, BGobj, by using either of the following syntaxes:

set(BGobj.nodes(n), 'PropertyName', PropertyValue)

BGobj.nodes(n).PropertyName = PropertyValue

Tip   To specify properties of a node using the node's ID, use the getnodesbyid function to create a handle for the node: nodehandle = getnodesbyid(BGobj, NodeID) Then use the handle for the node in either of the following syntaxes: set(nodehandle, 'PropertyName', PropertyValue) nodehandle.PropertyName = PropertyValue

Specifying Properties of an Edge of a Biograph Object

You can set a specific property of the nth edge of a biograph object, BGobj, by using either of the following syntaxes:

set(BGobj.edges(n), 'PropertyName', PropertyValue)

BGobj.edges(n).PropertyName = PropertyValue

Tip   To specify properties of an edge using the source and sink node's ID's, use the getedgesbynodeid function to create a handle for the edge: edgehandle = getedgesbynodeid(BGobj, SourceNodeID, ... SinkNodeID) Then use the handle for the edge in either of the following syntaxes: set(edgehandle, 'PropertyName', PropertyValue) edgehandle.PropertyName = PropertyValue

See Also

Bioinformatics Toolbox functions: biograph (object constructor),

Bioinformatics Toolbox methods of a biograph object: allshortestpaths, conncomp, dolayout, get, getancestors, getdescendants, getedgesbynodeid, getmatrix, getnodesbyid, getrelatives, isdag, isomorphism, isspantree, maxflow, minspantree, set, shortestpath, topoorder, traverse, view

baselookup

biograph

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