Fabrice,
As you note that
pathview does not work with Biocarta or Reactome pathways directly at this
time. You may still work with them if you can parse these pathways into "graphNEL"
objects (defined in graph package). We may provide this functionality as an
explicit feature in future release of pathview.
The following
example shows you how to redo the pathview workflow step by step when you have
pathway data file parsed into a "graphNEL" object (gR1 below). HTH. 
Weijun Luo
 
xml.file=paste(kegg.dir,
"hsa04966.xml", sep="/")
gR1=pathview:::parseKGML2Graph2(xml.file,
genesOnly=FALSE, expand=FALSE, split.group=FALSE)
 
node.data=node.info(gR1)
plot.data.gene=node.map(mol.data=gse16873.d[,1],
node.data,
node.types="gene")
head(plot.data.gene)
cols.ts.gene=node.color(plot.data.gene,
limit=1, bins=10)
head(cols.ts.gene)
 
pv.pars=
keggview.graph(plot.data.gene=plot.data.gene,
cols.ts.gene=cols.ts.gene,
node.data=node.data, path.graph=gR1,
pathway.name="hsa04966",
sign.pos="bottomleft")
	[[alternative HTML version deleted]]

