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CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices

Similarity and distance matrices are general data structures that describe reciprocal relationships between the objects within a given dataset. Commonly used methods for representation of these matrices include heatmaps, hierarchical trees, dimensionality reduction, and various types of networks. Ho...

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Detalles Bibliográficos
Autores principales: Baker, Frazier N., Porollo, Aleksey
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798608/
https://www.ncbi.nlm.nih.gov/pubmed/29423399
http://dx.doi.org/10.3390/data3010004
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author Baker, Frazier N.
Porollo, Aleksey
author_facet Baker, Frazier N.
Porollo, Aleksey
author_sort Baker, Frazier N.
collection PubMed
description Similarity and distance matrices are general data structures that describe reciprocal relationships between the objects within a given dataset. Commonly used methods for representation of these matrices include heatmaps, hierarchical trees, dimensionality reduction, and various types of networks. However, despite a well-developed foundation for the visualization of such representations, the challenge of creating an interactive view that would allow for quick data navigation and interpretation remains largely unaddressed. This problem becomes especially evident for large matrices with hundreds or thousands objects. In this work, we present a web-based platform for the interactive analysis of large (dis-)similarity matrices. It consists of four major interconnected and synchronized components: a zoomable heatmap, interactive hierarchical tree, scalable circular relationship diagram, and 3D multi-dimensional scaling (MDS) scatterplot. We demonstrate the use of the platform for the analysis of amino acid covariance data in proteins as part of our previously developed CoeViz tool. The web-platform enables quick and focused analysis of protein features, such as structural domains and functional sites.
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spelling pubmed-57986082018-03-01 CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices Baker, Frazier N. Porollo, Aleksey Data (Basel) Article Similarity and distance matrices are general data structures that describe reciprocal relationships between the objects within a given dataset. Commonly used methods for representation of these matrices include heatmaps, hierarchical trees, dimensionality reduction, and various types of networks. However, despite a well-developed foundation for the visualization of such representations, the challenge of creating an interactive view that would allow for quick data navigation and interpretation remains largely unaddressed. This problem becomes especially evident for large matrices with hundreds or thousands objects. In this work, we present a web-based platform for the interactive analysis of large (dis-)similarity matrices. It consists of four major interconnected and synchronized components: a zoomable heatmap, interactive hierarchical tree, scalable circular relationship diagram, and 3D multi-dimensional scaling (MDS) scatterplot. We demonstrate the use of the platform for the analysis of amino acid covariance data in proteins as part of our previously developed CoeViz tool. The web-platform enables quick and focused analysis of protein features, such as structural domains and functional sites. 2018-01-13 2018-03 /pmc/articles/PMC5798608/ /pubmed/29423399 http://dx.doi.org/10.3390/data3010004 Text en Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Baker, Frazier N.
Porollo, Aleksey
CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices
title CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices
title_full CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices
title_fullStr CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices
title_full_unstemmed CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices
title_short CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices
title_sort coeviz: a web-based integrative platform for interactive visualization of large similarity and distance matrices
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798608/
https://www.ncbi.nlm.nih.gov/pubmed/29423399
http://dx.doi.org/10.3390/data3010004
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