
Dear BioC users,

Is it possible to make a hierarchical graph with the root at the top?

	The code I used so far is something like:
	
	library(GOstats)
	library(Rgraphviz)
	goid <- c("GO:0006882", "GO:0016049")
	basic_graph <- GOGraph(goid, GOBPPARENTS)
	Attrs <- list()
	node_color <- c(rep("red",length(nodes(basic_graph))))
	Attrs$fillcolor <- node_color
	node_fontsize <- c(rep(40,length(nodes(basic_graph))))
	Attrs$fontsize <- node_fontsize
	node_shape <- rep("ellipse", length(nodes(basic_graph)))
	Attrs$shape <- node_shape
	node_fixedsize <- rep(FALSE, length(nodes(basic_graph)))
	Attrs$fixedsize <- node_fixedsize
	Attrs <- lapply(Attrs, function(x) {
		names(x) <- nodes(basic_graph)
		x
		})
	basic_nodes <- buildNodeList(basic_graph, nodeAttrs = Attrs)
	basic_edges <- buildEdgeList(basic_graph)
	colored_graph <- agopen(name = "foo", nodes = basic_nodes, edges =
basic_edges, edgeMode = "undirected")
	plot(colored_graph)
This last line will show a graph with the root at the bottom and the most
specific GOs at the top. Also plot(basic_graph) will show such a graph (but
with the standard attributes like white nodes in the shape of a circle etc).
I would like to show it up side down (root at the top). 
I can specify a layout when plotting the object called "basic_graph" using
the plot() function. The layouts I know are dot (default), neato, twopi,
circo and fdp.  However, these options do not result in what I have in mind.
So far, I have not yet found the parameter(s) which define(s) the position
of a node (e.g. x,y coordinates) on the plot. Could anyone give me a hint?
Thanks in advance!
Best regards,
An
Scientist Functional Genomics





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