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Pathview package (version 1.10.0) was updated substantially with the recent Bioc 3.2 release. We fixed several important problems reported with pathview1.8.0: 1) the colorless pathway graphs on some Linux platforms; 2) no/empty XML files downloaded for some general pathways (01200, 01210 etc). Below is a list of important updates/additions in Pathview 1.10.0. Please check out the new version, for more info:http://bioconductor.org/packages/rel.../pathview.html
Major updates with Pathview 1.10.0:
o pathview can accept a vector of multiple pathway ids, and map/render the user data onto all these pathways in one call.
o one extra column "all.mapped" was added to pathview output data.frames as to show all the gene/compound IDs mapped to each node.
o add geneannot.map as a generic function for gene ID or annotation mapping.
o sim.mol.data now generate data with all major gene ID types for all 19 species in bods, not just human.
o download.kegg now let the user to choose from xml, png or both file types to download for each input pathway. In the meantime, it uses the KEGG REST API instead of the classical KEGG download links. All potential pathways including the general pathways can be downloaded this way.
Major updates with Pathview 1.10.0:
o pathview can accept a vector of multiple pathway ids, and map/render the user data onto all these pathways in one call.
o one extra column "all.mapped" was added to pathview output data.frames as to show all the gene/compound IDs mapped to each node.
o add geneannot.map as a generic function for gene ID or annotation mapping.
o sim.mol.data now generate data with all major gene ID types for all 19 species in bods, not just human.
o download.kegg now let the user to choose from xml, png or both file types to download for each input pathway. In the meantime, it uses the KEGG REST API instead of the classical KEGG download links. All potential pathways including the general pathways can be downloaded this way.