pwayGraph-class {pathRender}R Documentation

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
edgemode:
Object of class "character" directed, typically
edgeData:
Object of class "attrData" relationship attributes
nodeData:
Object of class "attrData" node attributes
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]

[Package pathRender version 1.10.0 Index]