Last data update: 2014.03.03

R: plot a gene network, coloring nodes according to relative...
plotExGraphR Documentation

plot a gene network, coloring nodes according to relative expression values

Description

plot a gene network, coloring nodes according to relative expression values

Usage

plotExGraph(g, es, sampind=1, pal=colorRampPalette(brewer.pal(9, "Blues"))(length(nodes(g))), attgen=pwayRendAttrs)

Arguments

g

graph representing a gene network

es

an ExpressionSet instance

sampind

sample to be used to obtain relative expression values

pal

palette for coloring the nodes

attgen

attribute generating function

Details

plots a colored network on the current graphics display

Value

as returned by Rgraphviz plot method for graphNEL instances

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

library(graph)
data(pancrCaIni)
library(ALL)
data(ALL)
library(hgu95av2.db)
collap1 = reduceES( ALL, nodes(pancrCaIni), revmap(hgu95av2SYMBOL), "symbol", mean )
library(RColorBrewer)
plotExGraph( pancrCaIni, collap1, 1 )

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/plotExGraph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotExGraph
> ### Title: plot a gene network, coloring nodes according to relative
> ###   expression values
> ### Aliases: plotExGraph
> ### Keywords: models
> 
> ### ** Examples
> 
> library(graph)
> data(pancrCaIni)
> library(ALL)
> data(ALL)
> library(hgu95av2.db)
Loading required package: org.Hs.eg.db


> collap1 = reduceES( ALL, nodes(pancrCaIni), revmap(hgu95av2SYMBOL), "symbol", mean )
> library(RColorBrewer)
> plotExGraph( pancrCaIni, collap1, 1 )
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>