R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Render a laid out graph object

renderGraph

R Documentation

Render a laid out graph object

Description

This method uses the renderInfo slot of a graph object to render it on a plotting device. The graph must have been laid out using the layoutGraph function before.

Usage


## S4 method for signature 'graph'
renderGraph(x, ..., drawNodes="renderNodes", drawEdges=renderEdges, graph.pars=list())

Arguments

`x`	An object derived from class `graph`
`drawNodes`	A function that is used for the node rendering. The details of its API are still undecided, so far the input to the function is the (laid out) graph object. Defaults to `renderNodes`, which is not exported in the name space (type `Rgraphviz:::renderNodes` to see the function definition). This default function knows how to draw node shapes of type `box`, `rectangle`, `ellipse`, `plaintext`, `circle` and `triangle`. In addition, an arbitrary user-defined function can be passed on to draw the node. This function needs to be able to deal with the following arguments: a two-by-two matrix of the bounding box for the respective node, and `labelX`, `labelY`, `fill`, `col`, `lwd`, `lty`, `textCol`, `style`, `label` and `fontsize`, which are all defined by the layout algorithm or are graphical `nodeRenderInfo` parameters.
`drawEdges`	A function that is used for the edge rendering. Defaults to `renderEdges`. Currently, this function can draw different types of arrowheads: `open`, `normal`, `dot`, `odot`, `box`, `obox`, `tee`, `diamond`, `odiamond` and `none`. In addition, a user-defined function can be passed as `arrowhead` or `arrowtail` parameters which needs to be able to deal with 4 arguments: A list of xy coordinates for the center of the arrowhead, and the graphical parameters `col`, `lwd` and `lty`.
`graph.pars`	A list of rendering parameters to use as defaults. Parameters that have been explicitely set using `nodeRenderInfo`, `edgeRenderInfo` or `graphRenderInfo` take precendence. If not explicitely supplied, the value of a call to `graph.par` is used. This design allows to set session-wide defaults.
`...`	further arguments

Details

This method can render graph objects that have previously been laid out using the function layoutGraph. The details for user defined node drawing remain to be decided.

Value

An object derived from class graph with information about the coordinates of the nodes in the coordinate system of the plotting device added to the renderInfo slot.

Author(s)

Florian Hahne

Examples


set.seed(123)
V <- letters[1:5]
M <- 1:2
g1 <- randomGraph(V, M, 0.5)
edgemode(g1) <- "directed"
x <- layoutGraph(g1)
renderGraph(x)

## one of Graphviz's additional layout algorithms
x <- layoutGraph(g1, layoutType="neato")
renderGraph(x)

## some tweaks to Graphviz's node and edge attributes,
## including a user-defined arrowhead and node shape functions.
myArrows <- function(x, ...)
{
for(i in 1:4)
points(x,cex=i)
}

myNode <- function(x, col, fill, ...)
symbols(x=mean(x[,1]), y=mean(x[,2]), thermometers=cbind(.5, 1,
runif(1)), inches=0.5,
fg=col, bg=fill, add=TRUE)

eAtt <- list(arrowhead=c("a~b"=myArrows, "b~d"="odiamond", "d~e"="tee"))
nAtt <- list(shape=c(d="box", c="ellipse", a=myNode))
edgemode(g1) <- "directed"
x <- layoutGraph(g1, edgeAttrs=eAtt, nodeAttrs=nAtt, layoutType="neato")
renderGraph(x)

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(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, 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: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Rgraphviz/renderGraph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: renderGraph
> ### Title: Render a laid out graph object
> ### Aliases: renderGraph renderGraph,graph-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> set.seed(123)
> V <- letters[1:5]
> M <- 1:2
> g1 <- randomGraph(V, M, 0.5)
> edgemode(g1) <- "directed"
> x <- layoutGraph(g1)
> renderGraph(x)
> 
> ## one of Graphviz's additional layout algorithms
> x <- layoutGraph(g1, layoutType="neato")
> renderGraph(x)
> 
> ## some tweaks to Graphviz's node and edge attributes,
> ## including a user-defined arrowhead and node shape functions.
> myArrows <- function(x, ...)
+ {
+ for(i in 1:4)
+ points(x,cex=i)
+ }
> 
> myNode <- function(x, col, fill, ...)
+ symbols(x=mean(x[,1]), y=mean(x[,2]), thermometers=cbind(.5, 1,
+ runif(1)), inches=0.5,
+ fg=col, bg=fill, add=TRUE)
> 
> eAtt <- list(arrowhead=c("a~b"=myArrows, "b~d"="odiamond", "d~e"="tee"))
> nAtt <- list(shape=c(d="box", c="ellipse", a=myNode))
> edgemode(g1) <- "directed"
> x <- layoutGraph(g1, edgeAttrs=eAtt, nodeAttrs=nAtt, layoutType="neato")
> renderGraph(x)
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>