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A universal tool for visualisation of networks and trees in Python.

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Bibliographic Details
Title: A universal tool for visualisation of networks and trees in Python.
Authors: Zanini F; School of Clinical Medicine, University of New South Wales, Sydney, New South Wales, 2052, Australia.; Ecology & Evolution Research Centre, University of New South Wales, Sydney, NSW, 2052, Australia.; UNSW Cellular Genomics Futures Institute, UNSW, NSW, 2052, Australia.
Source: F1000Research [F1000Res] 2025 Dec 09; Vol. 14, pp. 1377. Date of Electronic Publication: 2025 Dec 09 (Print Publication: 2025).
Publication Type: Journal Article
Language: English
Journal Info: Publisher: F1000 Research Ltd Country of Publication: England NLM ID: 101594320 Publication Model: eCollection Cited Medium: Internet ISSN: 2046-1402 (Electronic) Linking ISSN: 20461402 NLM ISO Abbreviation: F1000Res Subsets: MEDLINE
Imprint Name(s): Original Publication: London : F1000 Research Ltd
MeSH Terms: Software* , Computer Graphics* , Programming Languages*
Abstract: 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 igraph and NetworkX, 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: iplotx 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: iplotx 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 iplotx 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, iplotx offers broader interoperability, richer styling, a large gallery of examples, and extensive code testing. This makes iplotx a robust choice for the visualisation of any networks and trees in biomedicine and beyond.
(Copyright: © 2025 Zanini F.)
Competing Interests: No competing interests were disclosed.
Contributed Indexing: Keywords: graphs; interactions.; networks; phylogenetics; plotting; trees; visualisation
Entry Date(s): Date Created: 20260302 Date Completed: 20260307 Latest Revision: 20260307
Update Code: 20260307
PubMed Central ID: PMC12946695
DOI: 10.12688/f1000research.173131.1
PMID: 41768044
Database: MEDLINE
Description
Abstract: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 igraph and NetworkX, 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.<br />Methods: iplotx 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.<br />Results: iplotx 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 iplotx include biomolecular and gene regulatory networks, protein-protein interactions, biochemical pathways, ecological networks, phylogenetics, and extend beyond biomedicine into economics, social, and transportation sciences.<br />Conclusions: Compared to extant software, iplotx offers broader interoperability, richer styling, a large gallery of examples, and extensive code testing. This makes iplotx a robust choice for the visualisation of any networks and trees in biomedicine and beyond.<br /> (Copyright: © 2025 Zanini F.)
ISSN:2046-1402
DOI:10.12688/f1000research.173131.1