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]]