plotKEGGgraph: Plot KEGG graph with Rgraphviz

In KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

Description

The function provides a simple interface to Rgraphviz to render KEGG graph with custom styles.

KEGGgraphLegend gives the legend of KEGG graphs

Usage

plotKEGGgraph(graph, y = "neato", shortLabel = TRUE,
useDisplayName=TRUE, nodeRenderInfos,  ...)
KEGGgraphLegend()

Arguments

graph	A KEGG graph, by calling parseKGML2Graph
y	the layout method, neato by default
shortLabel	logical, should be short label used instead of full node name?
useDisplayName	logical, should the labels of nodes rendered as the 'display name' specified in the KGML file or render them simply with the node names?
nodeRenderInfos	List of node rendering info
...	Other functions passed to renderGraph, not implemented for now

Details

Users are not restricted to this function, alternatively you can choose other rendering functions.

Value

The graph after layout and rendering is returned.

Author(s)

Jitao David Zhang mailto:[e-mail]

Examples

opar <- par(ask=TRUE)
sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
gR <- parseKGML2Graph(sfile,expandGenes=TRUE)
subs <-  c("hsa:1432",edges(gR)$`hsa:1432`,
	   "hsa:5778","hsa:5801","hsa:84867",
	   "hsa:11072","hsa:5606","hsa:5608",
	   "hsa:5494","hsa:5609")
gR.sub <- subGraph(subs, gR)
if(require(Rgraphviz))
  plotKEGGgraph(gR.sub)

KEGGgraphLegend()
par(opar)

Example output

Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

Loading required package: Rgraphviz
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, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: grid

KEGGgraph documentation built on Nov. 8, 2020, 5:42 p.m.