Example 5: showing a path

An undirected graph with 6 nodes, 8 edges, and a path between nodes marked out by red edges with line width of 3.

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 f;
  
  //edges        
  a -- b[color=red,penwidth=3.0]; // red 3 width line along desired path
  b -- c; 
  c -- d[color=red,penwidth=3.0]; 
  d -- e; 
  e -- f; 
  a -- d; 
  b -- d[color=red,penwidth=3.0]; 
  c -- f[color=red,penwidth=3.0]; 
}

R code for Rgraphviz and gridGraphviz:

# load Rgraphviz library
library(Rgraphviz)

# nodes
nodes <- letters[1:6]

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

graph <- new("graphNEL", nodes=nodes, edgeL=edgeList, edgemode="undirected")
graph <- layoutGraph(graph)

Graph rendering:

graphviz

Rgraphviz

gridGraphviz (old)

gridGraphviz (new)

>> neato -Tpng ex5.dot -o ex5.png

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

# mark out desired path
for (i in c(1, 4:6)) {
  AgEdge(rag)[[i]]@lwd <- 3
  AgEdge(rag)[[i]]@color <- "red"
}

#plot  
plot(rag)

library(gridGraphviz)

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

# mark out desired path
for (i in c(1, 4:6)) {
  AgEdge(rag)[[i]]@lwd <- 3
  AgEdge(rag)[[i]]@color <- "red"
}

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

library(gridGraphviz)

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

# mark out desired path
for (i in c(1, 4:6)) {
  AgEdge(rag)[[i]]@lwd <- 3
  AgEdge(rag)[[i]]@color <- "red"
}

#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.