pwayGraph-class: Class "pwayGraph" - extension to graphNEL for pathway...

In pathRender: Render molecular pathways

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 <[e-mail]>

Examples

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

pathRender documentation built on Nov. 8, 2020, 8:03 p.m.