Q:

How can I color nodes of a graphNEL graph? 

I'm using graphNEL objects from gRbase and Rgraphviz for plotting and would like to color the nodes of the graph in different (specified) colors when plotting.   For example, how could I plot this graph with a and b in blue and c and d in red? 
library(Rgraphviz)
library(gRbase)
mygraph = dag(~a:c + b:c + b:d)
plot(mygraph)

A:

This should work ;
nAttrs<-list()
nAttrs$color <- c(a = "blue", b = "blue", c = "red", d = "red")
plot(g1, nodeAttrs = nAttrs)

see also getDefaultAttrs() to get all the graph attributes with default values.