HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples

This paper presents an interactive visualization interface-HiPiler-for the exploration and visualization of regions-of-interest in large genome interaction matrices. Genome interaction matrices approximate the physical distance of pairs of regions on the genome to each other and can contain up to 3...

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Bibliographic Details
Published in:IEEE transactions on visualization and computer graphics 2018-01, Vol.24 (1), p.522-531
Main Authors: Lekschas, Fritz, Bach, Benjamin, Kerpedjiev, Peter, Gehlenborg, Nils, Pfister, Hanspeter
Format: Article
Language:English
Subjects:
Algorithm design and analysis
Bioinformatics
Biomedical Visualization
Columns (structural)
Data visualization
Exploration
Genomes
Genomics
Inspection
Interactive Small Multiples
Interviews
Matrix Comparison
Subject specialists
Visualization
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Summary:This paper presents an interactive visualization interface-HiPiler-for the exploration and visualization of regions-of-interest in large genome interaction matrices. Genome interaction matrices approximate the physical distance of pairs of regions on the genome to each other and can contain up to 3 million rows and columns with many sparse regions. Regions of interest (ROIs) can be defined, e.g., by sets of adjacent rows and columns, or by specific visual patterns in the matrix. However, traditional matrix aggregation or pan-and-zoom interfaces fail in supporting search, inspection, and comparison of ROIs in such large matrices. In HiPiler, ROIs are first-class objects, represented as thumbnail-like "snippets". Snippets can be interactively explored and grouped or laid out automatically in scatterplots, or through dimension reduction methods. Snippets are linked to the entire navigable genome interaction matrix through brushing and linking. The design of HiPiler is based on a series of semi-structured interviews with 10 domain experts involved in the analysis and interpretation of genome interaction matrices. We describe six exploration tasks that are crucial for analysis of interaction matrices and demonstrate how HiPiler supports these tasks. We report on a user study with a series of data exploration sessions with domain experts to assess the usability of HiPiler as well as to demonstrate respective findings in the data.
ISSN:1077-2626
1941-0506
DOI:10.1109/TVCG.2017.2745978