R: obtain a graph object corresponding to a cMAP pathway

graphcMAP

R Documentation

obtain a graph object corresponding to a cMAP pathway

Description

obtain a graph object corresponding to a cMAP pathway

Usage

graphcMAP(pname)

Arguments

pname

character token identifying a KEGG or cMAP pathway

Details

reuses code from pathRender but emits a
graphNEL-class instance with some
additional information for rendering

Value

an instance of pwayGraph, which extends graphNEL

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

G1 = graphcMAP("p53pathway")
G1
nodes(G1)
if (require(Rgraphviz)) plot(G1)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> library(pathRender)
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: RColorBrewer
Loading required package: cMAP
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Rgraphviz':
from, to
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pathRender/graphcMAP.Rd_%03d_medium.png", width=480, height=480)
> ### Name: graphcMAP
> ### Title: obtain a graph object corresponding to a cMAP pathway
> ### Aliases: graphcMAP
> ### Keywords: models
>
> ### ** Examples
>
> G1 = graphcMAP("p53pathway")
> G1
A pwayGraph graph with directed edges
Number of Nodes = 22
Number of Edges = 27
> nodes(G1)
[1] "100878" "101472" "101132" "100931" "101129" "101183" "101131" "101064"
[9] "101474" "100131" "101065" "101134" "101475" "101135" "100127" "101136"
[17] "101176" "101130" "101473" "100398" "100515" "101133"
> if (require(Rgraphviz)) plot(G1)
>
>
>
>
>
> dev.off()
null device
1
>