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Updated: Jun 3, 2025

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Marsilea: an intuitive generalized paradigm for composable visualizations.

Yimin Zheng1,2,3,4,5, Zhihang Zheng6, André F Rendeiro7,8

  • 1Cancer Centre, University of Macau, Taipa, Macau SAR.

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Summary

Biological data visualization faces challenges with complex datasets. The novel cross-layout paradigm and Marsilea tool offer an integrated approach for enhanced biological data visualization and interrelation insights.

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Area of Science:

  • Bioinformatics
  • Data Visualization
  • Computational Biology

Background:

  • Biological datasets are increasingly complex, challenging traditional visualization methods.
  • Single-data plots or simple juxtapositions are insufficient for capturing intricate dataset relationships.

Purpose of the Study:

  • Introduce a novel visualization paradigm, "cross-layout," to address limitations in biological data visualization.
  • Present "Marsilea," a Python-based implementation for creating cross-layout visualizations.

Main Methods:

  • Developed the "cross-layout" paradigm, integrating multiple plot types in a cross-like structure.
  • Created "Marsilea" with programmatic and web-based interfaces for user accessibility.
  • Implemented secondary plots surrounding a central main plot for contextualization.

Main Results:

  • The cross-layout paradigm effectively integrates multiple data types for enhanced contextualization.
  • Marsilea provides a customizable and intuitive tool for biological data visualization.
  • The approach facilitates deeper insights into dataset interrelations.

Conclusions:

  • The cross-layout paradigm and Marsilea offer a significant advancement in biological data visualization.
  • This integrated approach supports users of all experience levels in exploring complex biological data.
  • The customizable and intuitive nature of the tool promotes broader adoption and application in the field.