Article
Biochemistry & Molecular Biology
Kerry A. Mullan, Liesl M. Bramberger, Prithvi Raj Munday, Gabriel Goncalves, Jerico Revote, Nicole A. Mifsud, Patricia T. Illing, Alison Anderson, Patrick Kwan, Anthony W. Purcell, Chen Li
Summary: ggVolcanoR is an R-based Shiny application that allows customizable generation and visualization of volcano plots, correlation plots, upset plots, and heatmaps for differential expression datasets. It provides practical options for analyzing and comparing dysregulated genes/proteins across multiple datasets, and offers a downloadable list of filtered dysregulated expression data for downstream pathway analysis. The source code is available on GitHub and a webserver is freely accessible for academic purposes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Computer Science, Software Engineering
Bo Jiao, Xin Lu, Jingbo Xia, Brij Bhooshan Gupta, Lei Bao, Qingshan Zhou
Summary: This paper proposes a hierarchical structure model and a corresponding hierarchical structure sampling algorithm for sampling large-scale scale-free graphs in visualization. The algorithm can preserve the core community structure, important minority structures, and the connection relationship between low-degree nodes in the graph.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Computer Science, Software Engineering
Tom Horak, Philip Berger, Heidrun Schumann, Raimund Dachselt, Christian Tominski
Summary: Responsive matrix cells are local zoomable regions in a matrix that offer auxiliary facilities for data exploration and editing for multivariate graphs, adapting their visual contents based on cell location, available display space, and user tasks.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Article
Computer Science, Information Systems
Yan Zheng, Yi Ou, Alexander Lex, Jeff M. Phillips
Summary: The size of large, geo-located datasets has reached a scale where visualization of all data points is inefficient, leading to the need for subsampling methods. This study introduces a spatial data subsampling method suitable for very large datasets, showing it to be more accurate than random sampling. Additionally, a method is presented to ensure that the truncation of low values in the sampled data does not omit any regions above the desired threshold.
IEEE TRANSACTIONS ON BIG DATA
(2021)
Article
Biochemical Research Methods
Max Franz, Christian T. Lopes, Dylan Fong, Mike Kucera, Manfred Cheung, Metin Can Siper, Gerardo Huck, Yue Dong, Onur Sumer, Gary D. Bader
Summary: Cytoscape.js is an open-source graph library implemented in JavaScript. It can be used as a visualization software component to render interactive graphs in web browsers, or in a headless manner for server-side graph operations with Node.js.
Article
Biochemical Research Methods
Stefan Roder, Gunda Herberth, Ana C. Zenclussen, Mario Bauer
Summary: EpiVisR is a tool for visualizing epigenetic research, allowing users to select and visualize combinations of traits and differentially methylated probes/regions to gain insights from existing data.
BMC BIOINFORMATICS
(2022)
Article
Computer Science, Software Engineering
Daniel Reimann, Nilam Ram, Robert Gaschler
Summary: Scatterplots overlayed with a nonlinear model enable visual estimation of model-data fit. Although statistical fit is calculated using vertical distances, viewers' subjective fit is often based on shortest distances. Our results suggest that adding vertical lines (lollipops) supports more accurate fit estimation in the steep area of model curves (https://osf.io/fybx5/).
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Computer Science, Information Systems
Ilias Kalamaras, Konstantinos Glykos, Vasilis Megalooikonomou, Konstantinos Votis, Dimitrios Tzovaras
Summary: This paper proposes a graph-based data visualization method that can effectively explore large datasets and sensitive data. By graphically presenting patient datasets, the method helps medical professionals and researchers understand data distribution and characteristics.
MULTIMEDIA TOOLS AND APPLICATIONS
(2022)
Review
Computer Science, Information Systems
Prerna Mishra, Santosh Kumar, Mithilesh Kumar Chaube
Summary: Graph data extraction, interpretation, and summarization using deep learning-based methods have become important for understanding heterogeneous data. This paper provides an overview of quantitative and statistical approaches for learning and understanding different aspects of graph data, as well as their influence on visualization and upcoming research areas.
MULTIMEDIA TOOLS AND APPLICATIONS
(2023)
Article
Computer Science, Artificial Intelligence
Wilson E. Marcilio-Jr, Danilo M. Eler, Fernando Paulovich, Jose F. Rodrigues-Jr, Almir O. Artero
Summary: In this study, a scatter plot-based multilevel approach is proposed to display dimensionality reduction results and address clutter-related problems in visualizing large datasets. The technique uses sampling selection on scatter plots to reduce visual clutter and guide users through exploratory tasks. The effectiveness of the approach is demonstrated through a use case and a user experiment.
Review
Automation & Control Systems
Resul Das, Mucahit Soylu
Summary: This comprehensive review provides an in-depth analysis of the role of graph theory and graph visualization in scientific studies. It explores different graph types, special graphs, and the challenges and advancements in graph visualization techniques. The review serves as a valuable resource for researchers to understand the principles and applications of graphs in diverse scientific disciplines.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2023)
Article
Biochemical Research Methods
Qiaonan Duan, Weiyi Wang, Feiling Feng, Xiaoqing Jiang, Hao Chen, Dadong Zhang, Tongyi Zhang
Summary: Comut-viz is a highly responsive and extensible web app for creating comutation plots. It provides customization for frequently adjusted features and accepts large genomic files as input. It is suitable for genomic studies with more than a thousand samples.
BMC BIOINFORMATICS
(2023)
Article
Computer Science, Software Engineering
Zipeng Liu, Yang Wang, Juergen Bernard, Tamara Munzner
Summary: This article introduces a method to correspond an input graph to its node embedding and proposes an interactive multi-view interface called CorGIE to implement this method. The functionality and usability of CorGIE are evaluated by using K-hop graph layout to show topological neighbors and clustering structure.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2022)
Article
Mathematics, Applied
Nate Strawn
Summary: The efficiency of modern computer graphics allows us to explore and visualize collections of space curves simultaneously. By constructing computationally inexpensive 3D extensions of scatterplots of curves, we can mitigate the issue of visual clutter and achieve clearer visualization across an entire dataset. This is done by parametrizing optimal linear isometrics and constructing unit-length 3D curves called filaments. Filament plots, generated from Bishop frames induced by 3D scatterplots, provide a clearer visualization and avoid visual clutter.
APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS
(2022)
Article
Computer Science, Software Engineering
Youjia Zhou, Archit Rathore, Emilie Purvine, Bei Wang
Summary: We explore hypergraph visualization through topological simplification using tools from topological data analysis. By transforming a hypergraph into its graph representations, we can simplify the hypergraph based on the simplification of the graph representation. Our proposed approaches allow for the combination of vertices belonging to similar sets of hyperedges and the merging of hyperedges sharing similar sets of vertices. These approaches are general, mathematically justifiable, and provide a unified framework for both vertex and hyperedge simplification.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
