agopenTrue: A function to obtain a laidout 'Ragraph' object

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

This function is a wrapper for the Rgraphviz function agopen and will produce a laidout Ragraph object with layout more true to the result produced by graphviz.

Usage

1
2
3
4
agopenTrue(graph, name, nodes, edges, kind = NULL, layoutType = "dot", 
           attrs = list(), nodeAttrs = list(), edgeAttrs = list(),
           subGList = list(), edgeMode = edgemode(graph),
           recipEdges = c("combined", "distinct"))

Arguments

graph

An object of class graphNEL

nodes

A list of pNode objects

edges

A list of pEdge objects

name

The name of the graph

kind

The type of graph

layoutType

Defines the layout engine. Defaults to dot, and see graphvizCapabilities()$layoutTypes for possible values.

attrs

A list of graphviz attributes

nodeAttrs

A list of specific node attributes

edgeAttrs

A list of specific edge attributes

subGList

A list describing subgraphs for the graph parameter

edgeMode

Whether the graph is directed or undirected

recipEdges

How to handle reciprocated edges, defaults to combined

Details

As of Rgraphviz version 2.2.1 (2013-01-31) agopen:

This function returns an Ragraph object with graph and node sizes set by graphviz or by the user. It also ensures edge weight information is passed through.

Value

An object of class Ragraph

Author(s)

Ashley Noel Hinton

References

graphviz

See Also

agopen

Examples

1
2
3
4
5
6
7
8
gnel <- new("graphNEL",
            nodes=letters[1:3],
            edgeL=list(a=list(edges=c("b", "c")),
                       b=list(),
                       c=list()),
            edgemode="directed")
rag <- agopenTrue(gnel, "")
grid.graph(rag)

Example output

Loading required package: grid
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: Rgraphviz

gridGraphviz documentation built on May 2, 2019, 2:44 a.m.