plotAnnGraph: Visualize annotated pathway graphs

In SubpathwayLNCE: Identify Signal Subpathways Competitively Regulated by LncRNAs Based on ceRNA Theory

Description

Visualize annotated pathway graphs.

Usage

	plotAnnGraph(pathwayId,graphList,ann,gotoKEGG=FALSE,orgSpecific=TRUE,
	displayInR=TRUE,match=TRUE,vertex.frame.color="red",...)

Arguments

pathwayId	A character vector of pathway identifier, e.g., c("path:00010","path:00020").
graphList	A graph list.
ann	A list, e.g., the return value of the function identifyLncGraphW.
gotoKEGG	A logical. If TRUE, go to KEGG web site. The identified nodes are colored red.
orgSpecific	A logical.
match	A logical.
displayInR	A logical. If TRUE, display pathway graphs on the device.
vertex.frame.color	A character defining the frame color of the nodes which represent the annotated nodes in the pathway.
...	The arguments passed to or from methods. See plotGraphL, plot.igraph and see plot.

Details

The function can visualize the annotated pathway (or subpathways) graphs. The red nodes in the result graph represent the nodes which include the submitted molecules.

Author(s)

Xinrui Shi, Chunquan Li, Xia Li

See Also

plotGraphL,identifyLncGraphW,printGraphW

Examples

## Not run: 
### Integrate lncRNAs of competitive regulation into KEGG pathway graphs ###
  LncGenePairs<-GetExampleData(exampleData="LncGenePairs")
  g2<-GetExampleData(exampleData="g2")
  interUMGraph<-getInteGraphList(g2,LncGenePairs)
  interUMGraph<-getInteUMGraph(LncGenePairs)
### get user-interested lncRNAs and genes sets.
  geneLnc<-GetExampleData(exampleData="geneLnc")
# get locate subpathways.
  sub<-getLocSubGraphLnc(geneLnc,interUMGraph,type="gene_lncRNA",n=1,s=8)
  SubcodeLncResult<-identifyLncGraphW(geneLnc,sub,type="gene_lncRNA",bet=1)
  resultT<-printGraphW(SubcodeLncResult,detail=TRUE)
  plotAnnGraph("path:04020_1",sub,SubcodeLncResult,gotoKEGG=FALSE)


## End(Not run)

SubpathwayLNCE documentation built on May 1, 2019, 10:25 p.m.