Pathview is a novel R/Bioconductor package designed for pathway-based data integration and visualization. It maps and renders user data onto relevant pathway graphs, requiring only the user to supply their data and specify the target pathway. Pathview automatically downloads pathway graph data, parses the file, integrates user data, and renders the pathway graphs. Key features include: 1. **Full Accessible and Functional Pathway Visualization**: Adheres to human-readable pathway definitions and layouts, allowing modifications and customizations. 2. **Strong Data Integration Capacity**: Supports various data types, IDs, formats, attributes, and species, with extensive data mapping and integration support. 3. **Easy Automation and Integration**: Can be seamlessly integrated into automated pathway analysis pipelines and other tools in R/Bioconductor. Pathview is freely available under the GPLv3 license through Bioconductor and R-Forge. It is particularly useful for high-throughput data analysis, gene expression, genetic and GWAS, proteomic, and metabolomics data. The package includes four main functional modules: Downloader, Parser, Mapper, and Viewer. It can generate both KEGG and Graphviz views, supporting a wide range of data types and species. Pathview is open-source, automated, and error-resistant, making it suitable for integrated pathway or gene set analysis workflows.Pathview is a novel R/Bioconductor package designed for pathway-based data integration and visualization. It maps and renders user data onto relevant pathway graphs, requiring only the user to supply their data and specify the target pathway. Pathview automatically downloads pathway graph data, parses the file, integrates user data, and renders the pathway graphs. Key features include: 1. **Full Accessible and Functional Pathway Visualization**: Adheres to human-readable pathway definitions and layouts, allowing modifications and customizations. 2. **Strong Data Integration Capacity**: Supports various data types, IDs, formats, attributes, and species, with extensive data mapping and integration support. 3. **Easy Automation and Integration**: Can be seamlessly integrated into automated pathway analysis pipelines and other tools in R/Bioconductor. Pathview is freely available under the GPLv3 license through Bioconductor and R-Forge. It is particularly useful for high-throughput data analysis, gene expression, genetic and GWAS, proteomic, and metabolomics data. The package includes four main functional modules: Downloader, Parser, Mapper, and Viewer. It can generate both KEGG and Graphviz views, supporting a wide range of data types and species. Pathview is open-source, automated, and error-resistant, making it suitable for integrated pathway or gene set analysis workflows.