Last data update: 2014.03.03

R: Render pathways from cMAP
rendercMAPPathwayR Documentation

Render pathways from cMAP

Description

Build graphs based on pathway or interaction data from cMAP database, render them using Rgraphviz.

Usage

rendercMAPPathway(pname, ino=0) 

Arguments

pname

name of the pathway to render

ino

index of the interaction in the given pathway to render

Details

For a given pathway in cMAP database, we build a subgraph for each interaction in the pathway, join them together to form the graph for the complete pathway. The subgraphs for interactions and the graph for the pathway include info for rendering, such as labels/shapes/fillcolors for nodes, colors/styles/weights for edges. If user specifies an index of interaction, only the interaction is rendered. Otherwise, the complete pathway is rendered.

Value

None. A graphical output is presented.

Author(s)

Li Long <li.long@isb-sib.ch>

Examples

   rendercMAPPathway("plateletapppathway")
   rendercMAPPathway("plateletapppathway", 5)
   rendercMAPPathway("hsa00601")
   rendercMAPPathway("hsa00601", 10)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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/rendercMAP.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rendercMAPPathway
> ### Title: Render pathways from cMAP
> ### Aliases: rendercMAPPathway
> ### Keywords: graphs
> 
> ### ** Examples
> 
>    rendercMAPPathway("plateletapppathway")
[1] "BioCarta"
>    rendercMAPPathway("plateletapppathway", 5)
[1] "BioCarta"
>    rendercMAPPathway("hsa00601")
[1] "KEGG"
>    rendercMAPPathway("hsa00601", 10)
[1] "KEGG"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>