Pathview is an R/Bioconductor package for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines. Pathview provides three key features: (i) fully accessible and functional pathway visualization, adhering to human readable pathway definitions and layouts like KEGG. (ii) Strong data integration capacity, integrating and working with data of different types, IDs, formats, attributes, species, etc. (iii) Easy to automate and integrate with pathway analysis tools. Pathview supports data integration for gene expression, protein expression, metabolite level, genetic association, genomic variation, literature records, and other data types mappable to pathways. It can be directly used for metagenomic data when mapped to KEGG ortholog pathways. Pathview can be divided into four functional modules: Downloader, Parser, Mapper and Viewer. It generates both native KEGG view and Graphviz view for pathways. Both graph styles adhere to human readable pathway definitions and layouts, allowing proper modification and customization of node and edge attributes. KEGG view retains all pathway meta-data, while Graphviz view provides better control of node and edge attributes, better view of pathway topology and better understanding of pathway analysis statistics. Pathview is open source, fully automated and error-resistant. It can be easily integrated with other tools for automated and efficient pathway analysis pipelines. Pathview accommodates deficiencies in KEGG XML data files, correcting them or skipping problematic pathways with warnings. It uses the KEGGgraph package to parse KEGG XML data files. Pathview works with all types and species of KEGG pathways and plans to support pathways from Reactome and other databases in the future.Pathview is an R/Bioconductor package for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines. Pathview provides three key features: (i) fully accessible and functional pathway visualization, adhering to human readable pathway definitions and layouts like KEGG. (ii) Strong data integration capacity, integrating and working with data of different types, IDs, formats, attributes, species, etc. (iii) Easy to automate and integrate with pathway analysis tools. Pathview supports data integration for gene expression, protein expression, metabolite level, genetic association, genomic variation, literature records, and other data types mappable to pathways. It can be directly used for metagenomic data when mapped to KEGG ortholog pathways. Pathview can be divided into four functional modules: Downloader, Parser, Mapper and Viewer. It generates both native KEGG view and Graphviz view for pathways. Both graph styles adhere to human readable pathway definitions and layouts, allowing proper modification and customization of node and edge attributes. KEGG view retains all pathway meta-data, while Graphviz view provides better control of node and edge attributes, better view of pathway topology and better understanding of pathway analysis statistics. Pathview is open source, fully automated and error-resistant. It can be easily integrated with other tools for automated and efficient pathway analysis pipelines. Pathview accommodates deficiencies in KEGG XML data files, correcting them or skipping problematic pathways with warnings. It uses the KEGGgraph package to parse KEGG XML data files. Pathview works with all types and species of KEGG pathways and plans to support pathways from Reactome and other databases in the future.