KEGG pathway display with DiagrammeR

# install.packages('DiagrammeR')
# requires V8 package (in turn requires `apt-get install libv8-dev`)

# source("http://bioconductor.org/bioclite.r")
# biocLite("KEGGgraph")
# biocLite('Rgraphviz')

# library('DiagrammeR')
# library('KEGGgraph')
# library('Rgraphviz')

Download your KGML (.xml) for the organism/pathway from KEGG, e.g. adenine pathway in S. cerevisiae:

KEGGgraph parses KEGG XML ("KGML") into graph models in R

# purine.kgml <- system.file("sce00230.xml", package="KEGGgraph")
# ^ did not work

purine.kgml <- "sce00230.xml"
purine.graph <- parseKGML2DataFrame(purine.kgml, genesOnly = FALSE)
# purine.graph is Formal class graphNEL

DiagrammeR works with DOT language graph specifications. graphViz can create these from this data frame (actually I think it's a Diagrammer function) :

nodes_edges <-
    graphviz_single_df(
        df = purine.graph,
        edge_between = c("from -> to"),
        node_attr = c("from:
                   shape = circle,
                   style = filled,
                   height = 2,
                   layer = 'all',
                   fontname = Helvetica,
                   fontsize = 42,
                   fillcolor = lightblue",
                      "to: 
                   shape = circle,
                   style = filled,
                   height = 1,
                   layer = 'all',
                   fontname = Helvetica,
                   fontsize = 0,
                   fillcolor = seagreen3"),
        edge_attr = "1:
                   color = #ff000040,
                   arrowhead = dot
                  "
    )

# this is for the radial plot (stolen from flights example)

grViz("
digraph adenine {

  # Graph statements
  graph [layout = twopi,
         overlap = false,
         fixedsize = true,
         ranksep = 11,
         outputorder = edgesfirst]

  # Nodes and edges
  @@1

}
[1]: nodes_edges
")