Easylayout: pacote R integrado à IDE para dispor grafos usando simulações de força

Abstract

Network visualization is a critical step for effective communication in various fields of knowledge, especially in life sciences. Currently, a gap separates network manipulation from network visualization in programming environments. Users constantly face the inconvenience of exporting network data to be laid out in external software, like Cytoscape and Gephi. We propose easylayout, a package that seamlessly bridges manipulation and visualization through the integration with the user’s IDE (e.g., RStudio, VSCode, Jupyter Notebook). It is not meant as another visualization library, but rather aims to standardize and interconnect existing libraries. The easylayout package receives an igraph object and serializes it into a web application integrated with the RStudio interface through a Shiny server. This web application provides an environment to lay out the network by simulating attraction and repulsion forces. There is an editing mode that allows users to move and rotate vertices. The development of easylayout aims for computational performance, so that even low-end devices are able to work with relatively large networks. One way this is done is by curating high-performing libraries like VivaGraphJS and d3-force. Once the user finishes tinkering the layout, it is sent back to the R session to be plotted through popular libraries like ggplot2 or even the base package itself. The current implementation focuses on the R ecosystem, but using web technologies makes it easily portable to similar environments, like Jupyter Notebooks. We expect this tool to reduce the time spent tweaking network layouts, allowing researches to generate more compelling figures. It is freely available under an MIT license on GitHub (https://github.com/dalmolingroup/easylayout). The package is implemented in R/Shiny and JavaScript/Svelte.