Class "pwayGraph" – extension to graphNEL for pathway rendering

Description

extension to graphNEL for pathway rendering

Objects from the Class

Objects can be created by calls of the form new("pwayGraph", nodes, edgeL, edgemode).

There is a plot method that will work reasonably well if the plotting surface is big enough.

Slots

pwaySource:

Object of class "character" KEGG or BIOCARTA

nodes:

Object of class "vector" pathway constituents in the native vocabulary

edgeL:

Object of class "list" constituent relations in the native vocabulary

edgeData:

Object of class "attrData" relationship attributes

nodeData:

Object of class "attrData" node attributes

renderInfo:

Object of class "renderInfo" render info

graphData:

Object of class "list" this holds the special rendering attributes for edges and nodes, for nodes it seems particularly important to have fixedsize = FALSE

Extends

Class graphNEL-class, directly. Class graph-class, by class "graphNEL", distance 2.

Methods

plot

signature(x = "pwayGraph"): renders the pathway

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

showClass("pwayGraph")
G1 = graphcMAP("stresspathway")
G1@graphData$nAttrs$labels[1:10]