Pathview provides strong support for data integration. Pathview uses KEGGgraph when parsing KEGG xml data files. However, Pathview downloads individual pathway graphs and data files through html access, which is freely available (for academic and non-commerical uses). Notice that KEGG requires subscription for FTP access since May 2011.

Hopefully, pathways from Reactome, NCI and other databases will be supported in the future. Currently only KEGG pathways are implemented. Graphviz view provides better control of node and edge attributes, better view of pathway topology, better understanding of the pathway analysis statistics.

This is important for human reading and interpretation of pathway biology. KEGG view keeps all the meta-data on pathways, spacial and temporal information, tissue/cell types, inputs, outputs and connections. Pathview generates both native KEGG view (in PNG format) and Graphviz view (in PDF format) for pathways.

Although built as a stand-alone program, pathview may seamlessly integrate with pathway (and functional) analysis tools for a large-scale and fully automated analysis pipeline. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and renders pathway graph with the mapped data. All users need is to supply their gene or compound data and specify the target pathway. It maps and renders user data on relevant pathway graphs. The pathview R package is a tool set for pathway based data integration and visualization.

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