Example 1: simple undirected graph

A simple undirected graph with 5 nodes and 6 edges. The graph has been rendered with graphviz in the Linux command line, and with R packages Rgraphviz, and gridGraphviz in R.

Graph declaration

In all cases the graph is explicitly declared with ellipse shaped nodes. The dot file edges are declared in alphabetical order as this is the (assumed) default for how Rgraphviz will pass edges internally to graphviz.

Dot file for graphviz:


graph {      
  node [shape=ellipse];
  
  // nodes
  a b c d e;
  
  // edges
  a -- b; 
  a -- c;
  a -- e;
  b -- c; 
  c -- d;
  c -- e; 
}

R code for Rgraphviz and gridGraphviz:

# load Rgraphviz library
library(Rgraphviz)

## Loading required package: graph
## Loading required package: grid

# define nodes and edges
nodes <- c("a", "b", "c", "d", "e")
edgeList <- list(a=list(edges=c("b", "c", "e")),
                 b=list(edges=c("a", "c")),
                 c=list(edges=c("a", "b", "d", "e")),
                 d=list(edges=c("c")),
                 e=list(edges=c("a", "c")))

# create graph object
graph <- new("graphNEL",
           nodes = nodes,
           edgeL = edgeList,
           edgemode = "undirected")

Graph rendering:

graphviz

Rgraphviz

gridGraphviz (old)

gridGraphviz (new)

>> dot -Tpng ex1.dot -o ex1.png

# create Ragraph object
rag <- agopen(graph, "", attrs=list(node=list(shape="ellipse")))

#plot  
plot(rag)

library(gridGraphviz)

# create Ragraph object
rag <- agopen(graph, "", attrs=list(node=list(shape="ellipse")))

#plot  
grid.graph(rag)

## Warning: Unsupported node shape; using 'box'
## Warning: Unsupported node shape; using 'box'
## Warning: Unsupported node shape; using 'box'
## Warning: Unsupported node shape; using 'box'
## Warning: Unsupported node shape; using 'box'

library(gridGraphviz)

# create Ragraph object
rag <- agopenTrue(graph, "", attrs=list(node=list(shape="ellipse")))

#plot  
grid.graph(rag)

Discussion

gridGraphviz (old) fails to produce ellipse shaped nodes, and produces "extra edges" which extend, in all cases, to the origin.