A universal tool for visualisation of networks and trees in Python

<ns3:p> Background Graphs or networks are ubiquitous data structures across scientific disciplines, from ecological and molecular to social networks. Visualisation is an important step to gain insight into network data, however most network analysis software packages, such as <ns3:italic>igraph</ns3:italic> and <ns3:italic>NetworkX</ns3:italic> , focus on statistical tools and offer limited visualisation options. Other packages offer powerful graphical user interfaces but rely on custom formats and implementations, which restricts interoperability with other scientific software. Methods <ns3:italic>iplotx</ns3:italic> is a Python software package designed to act as a universal visualiser for any network analysis package. A simple yet rich declarative style grammar enables customisation of any visual element including edge geometry, marker size and shape, labels, and groupings. Rendering relies on custom Matplotlib artists, which enables broad interoperability with other data visualisation libraries. Results <ns3:italic>iplotx</ns3:italic> supports eight different network and tree analysis packages (NetworkX, igraph, graph tool, Biopython, ETE, cogent3, dendropy, and scikit-bio) and implements a plug-in mechanism for universal input compatibility. It supports a wide spectrum of outputs including raster and vector images, animations, and interactive plots. The package implements unique features such as three-dimensional network visualisations and is fully compatible with the Python scientific software stack including seaborn, scipy, pandas, and Cartopy. Areas of application for <ns3:italic>iplotx</ns3:italic> include biomolecular and gene regulatory networks, protein-protein interactions, biochemical pathways, ecological networks, phylogenetics, and extend beyond biomedicine into economics, social, and transportation sciences. Conclusions Compared to extant software, <ns3:italic>iplotx</ns3:italic> offers broader interoperability, richer styling, a large gallery of examples, and extensive code testing. This makes <ns3:italic>iplotx</ns3:italic> a robust choice for the visualisation of any networks and trees in biomedicine and beyond. </ns3:p>