Web-based Interactive Visualization Research Articles

312 Statistical graphics and interactive visualization in animal science

Abstract Statistical graphics has advanced significantly in recent years with the development of statistical computing tools that allow us to create reports dynamically, facilitate reproducible research, and explore data interactively. In particular, data visualization is a fundamental aspect of big data analysis in animal science. However, the static nature of standard visualization limits the information that can be displayed and extracted. The objectives of this hands-on workshop are to learn how to utilize interactive visualization and investigate both global and local structures of graphs with useful zooming in and zooming out capabilities. We will use the Shiny R package, which is a web application framework for R. A Shiny application has great potential to deliver interactive data analysis and visualization in a web browser. Yet there is limited application of this type of tool in agricultural science. We will learn the capabilities of R Shiny and its use with example applications in animal science and how to aid scientific discoveries and decision-making processes using interactive data exploration tools. After taking this workshop, the participants will be able to understand the concept of R Shiny and develop a web-based interactive visualization tool. The interactive and integrative data visualization features embedded in Shiny applications offer a new resource for users to readily extract extensive information from complex data.

An Interactive Data Visualization Framework for Exploring Geospatial Environmental Datasets and Model Predictions

With the rise of large-scale environmental models comes new challenges for how we best utilize this information in research, management and decision making. Interactive data visualizations can make large and complex datasets easier to access and explore, which can lead to knowledge discovery, hypothesis formation and improved understanding. Here, we present a web-based interactive data visualization framework, the Interactive Catchment Explorer (ICE), for exploring environmental datasets and model outputs. Using a client-based architecture, the ICE framework provides a highly interactive user experience for discovering spatial patterns, evaluating relationships between variables and identifying specific locations using multivariate criteria. Through a series of case studies, we demonstrate the application of the ICE framework to datasets and models associated with three separate research projects covering different regions in North America. From these case studies, we provide specific examples of the broader impacts that tools like these can have, including fostering discussion and collaboration among stakeholders and playing a central role in the iterative process of data collection, analysis and decision making. Overall, the ICE framework demonstrates the potential benefits and impacts of using web-based interactive data visualization tools to place environmental datasets and model outputs directly into the hands of stakeholders, managers, decision makers and other researchers.

Interactive Web-based Data Visualization and Analysis Tool for Synthetizing on-farm Research Networks Data.

The on-farm research network concept enables a group of farmers to test new agricultural management practices under local conditions with support from local researchers or agronomists. Different on-farm trials based on the same experimental design are conducted over several years and sites to test the effectiveness of different innovative management practices aimed at increasing crop productivity and profitability. As a larger amount of historical trial data are being accumulated, data of all the trials require analyses and summarization. Summaries of on-farm trials are usually presented to farmers as individual field reports, which are not optimal for the dissemination of results and decision making. A more practical communication method is needed to enhance result communication and decision making. R Shiny is a new rapidly developing technology for turning R data analyses into interactive web applications. For the first time for on-farm research networks, we developed and launched an interactive web tool called ISOFAST using R Shiny. ISOFAST simultaneously reports all trial results about the same management practice to simplify interpretation of multi-site and multi-year summaries. We used a random-effects model to synthetize treatment differences at both the individual trial and network levels and generate new knowledge for farmers and agronomists. The friendly interface enables users to explore trial summaries, access model outputs, and perform economic analysis at their fingertips. This paper describes a case-study to illustrate how to use the tool and make agronomic management decisions based on the on-farm trial data. We also provided technical details and guidance for developing a similar interactive visualization tool customized for on-farm research network. ISOFAST is currently available at https://analytics.iasoybeans.com/cool-apps/ISOFAST/.

Visual exploration of Internet news via sentiment score and topic models

Analyzing and understanding Internet news are important for many applications, such as market sentiment investigation and crisis management. However, it is challenging for users to interpret a massive amount of unstructured text, to dig out its accurate meaning, and to spot noteworthy news events. To overcome these challenges, we propose a novel visualization-driven approach for analyzing news text. We first collect Internet news from different sources and encode sentences into a vector representation suitable for input to a neural network, which calculates a sentiment score, to help detect news event patterns. A subsequent interactive visualization framework allows the user to explore the development of and relationships between Internet news topics. In addition, a method for detecting news events enables users and domain experts to interactively explore the correlations between market sentiment, topic distribution, and event patterns. We use this framework to provide a web-based interactive visualization system. We demonstrate the applicability and effectiveness of our proposed system using case studies involving blockchain news.

A visual tool to explore the composition of international migration flows in the EU countries, 1998–2015

Background: Ternary plots can effectively display compositional data and help to understand its multidimensional patterns. However, they are currently greatly underused in demography. Objective: My goal is to develop an interactive web-based visualization of compositional data on international migration flows in order to compare its developments over time and across countries, and through this example demonstrate the utility of ternary diagrams. Methods: R Shiny framework is used to build a web application. Immigration and emigration flows in the EU Member States from 1998 to 2015 are grouped into three conventional categories (nationals of a reporting country, [other] EU nationals, and non-EU nationals) and presented on ternary diagrams. Results: Compositional data on migration flows can be effectively visualized using ternary plots. An interactive web application has been developed that allows comparative exploratory analysis of immigration and emigration composition and size in the EU countries over time. The impact of the entry of new countries to the EU can be assessed by comparing data referring to the EU composition of 28 Member States with data referring to the EU composition of the reference period. Conclusions: Ternary plots can facilitate compositional analysis of migration flows grouped into three categories. Contribution: I introduce ternary plots for an exploratory analysis of migration composition and provide an online tool to carry out illustrative exploration. Demographic analysis of compositional data can benefit from the wider use of such plots.

CiteFuse enables multi-modal analysis of CITE-seq data.

Multi-modal profiling of single cells represents one of the latest technological advancements in molecular biology. Among various single-cell multi-modal strategies, cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) allows simultaneous quantification of two distinct species: RNA and cell-surface proteins. Here, we introduce CiteFuse, a streamlined package consisting of a suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data. We demonstrate the capacity of CiteFuse to integrate the two data modalities and its relative advantage against data generated from single-modality profiling using both simulations and real-world CITE-seq data. Furthermore, we illustrate a novel doublet detection method based on a combined index of cell hashing and transcriptome data. Finally, we demonstrate CiteFuse for predicting ligand-receptor interactions by using multi-modal CITE-seq data. Collectively, we demonstrate the utility and effectiveness of CiteFuse for the integrative analysis of transcriptome and epitope profiles from CITE-seq data. CiteFuse is freely available at http://shiny.maths.usyd.edu.au/CiteFuse/ as an online web service and at https://github.com/SydneyBioX/CiteFuse/ as an R package. pengyi.yang@sydney.edu.au. Supplementary data are available at Bioinformatics online.

Triangulum City Dashboard: An Interactive Data Analytic Platform for Visualizing Smart City Performance

Cities are becoming smarter by incorporating hardware technology, software systems, and network infrastructure that provide Information Technology (IT) systems with real-time awareness of the real world. What makes a “smart city” functional is the combined use of advanced infrastructure technologies to deliver its core services to the public in a remarkably efficient manner. City dashboards have drawn increasing interest from both city operators and citizens. Dashboards can gather, visualize, analyze, and inform regional performance to support the sustainable development of smart cities. They provide useful tools for evaluating and facilitating urban infrastructure components and services. This work proposes an interactive web-based data visualization and data analytics toolkit supported by big data aggregation tools. The system proposed is a cloud-based prototype that supports visualization and real-time monitoring of city trends while processing and displaying large data sets on a standard web browser. However, it is capable of supporting online analysis processing by answering analytical queries and producing graphics from multiple resources. The aim of this platform is to improve communication between users and urban service providers and to give citizens an overall view of the city’s state. The conceptual framework and architecture of the proposed platform are explored, highlighting design challenges and providing insight into the development of smart cities. Moreover, results and the potential statistical analysis of important city services offered by the system are introduced. Finally, we present some challenges and opportunities identified through the development of the city data platform.

VisBicluster: A Matrix-Based Bicluster Visualization of Expression Data.

One of the main methods to analyze gene expression data is biclustering, a nonsupervised technique, which consists of selection subgroups of genes that co-expressed under subgroups of experimental conditions. A large number of biclustering algorithms have been developed to classify gene expression data. These algorithms can give as output a large number of overlapped biclusters, whose visualization still requires deeper studies. We present VisBicluster, a web-based interactive visualization tool for displaying biclustering results. The developed visualization technique consists of laying out the generated biclusters in a two-dimensional matrix where each bicluster is represented as a column and each overlap between a set of biclusters is represented as a row. A search interface for the user is developed to query the matrix of bicluster intersection and visualize the results matching the queries. Our tool supports many interactive features such as sorting, zooming, and details-on-demand. We proved the usefulness of VisBicluster with biclustering results from real and synthetic datasets. Besides, we performed a user study with 14 participants to illustrate the clarity and simplicity of overlap representation with our tool.

Real-time health monitoring through urine metabolomics

Current healthcare practices are reactive and based on limited physiological information collected months or years apart. By enabling patients and healthy consumers access to continuous measurements of health, wearable devices and digital medicine stand to realize highly personalized and preventative care. However, most current digital technologies provide information on a limited set of physiological traits, such as heart rate and step count, which alone offer little insight into the etiology of most diseases. Here we propose to integrate data from biohealth smartphone applications with continuous metabolic phenotypes derived from urine metabolites. This combination of molecular phenotypes with quantitative measurements of lifestyle reflect the biological consequences of human behavior in real time. We present data from an observational study involving two healthy subjects and discuss the challenges, opportunities, and implications of integrating this new layer of physiological information into digital medicine. Though our dataset is limited to two subjects, our analysis (also available through an interactive web-based visualization tool) provides an initial framework to monitor lifestyle factors, such as nutrition, drug metabolism, exercise, and sleep using urine metabolites.

Exploring Comorbidity Within Mental Disorders Among a Danish National Population

ImportanceIndividuals with mental disorders often develop comorbidity over time. Past studies of comorbidity have often restricted analyses to a subset of disorders and few studies have provided absolute risks of later comorbidity.ObjectivesTo undertake a comprehensive study of comorbidity within mental disorders, by providing temporally ordered age- and sex-specific pairwise estimates between the major groups of mental disorders, and to develop an interactive website to visualize all results and guide future research and clinical practice.Design, Setting, and ParticipantsThis population-based cohort study included all individuals born in Denmark between January 1, 1900, and December 31, 2015, and living in the country between January 1, 2000, and December 31, 2016. The analyses were conducted between June 2017 and May 2018.Main Outcomes and MeasuresDanish health registers were used to identify mental disorders, which were examined within the broad 10-level International Statistical Classification of Diseases and Related Health Problems, 10th Revision, subchapter groups (eg, codes F00-F09 and F10-F19). For each temporally ordered pair of disorders, overall and lagged hazard ratios and 95% CIs were calculated using Cox proportional hazards regression models. Absolute risks were estimated using competing risks survival analyses. Estimates for each sex were generated.ResultsA total of 5 940 778 persons were included in this study (2 958 293 men and 2 982 485 women; mean [SD] age at beginning of follow-up, 32.1 [25.4] years). They were followed up for 83.9 million person-years. All mental disorders were associated with an increased risk of all other mental disorders when adjusting for sex, age, and calendar time (hazard ratios ranging from 2.0 [95% CI, 1.7-2.4] for prior intellectual disabilities and later eating disorders to 48.6 [95% CI, 46.6-50.7] for prior developmental disorders and later intellectual disabilities). The hazard ratios were temporally patterned, with higher estimates during the first year after the onset of the first disorder, but with persistently elevated rates during the entire observation period. Some disorders were associated with substantial absolute risks of developing specific later disorders (eg, 30.6% [95% CI, 29.3%-32.0%] of men and 38.4% [95% CI, 37.5%-39.4%] of women with a diagnosis of mood disorders before age 20 years developed neurotic disorders within the following 5 years).Conclusions and RelevanceComorbidity within mental disorders is pervasive, and the risk persists over time. This study provides disorder-, sex-, and age-specific relative and absolute risks of the comorbidity of mental disorders. Web-based interactive data visualization tools are provided for clinical utility.

A hybrid approach for using programming exercises in introductory physics

Incorporating computer programming exercises into introductory physics is a delicate task that involves a number of choices that may have an effect on student learning. We present a “hybrid” approach that speaks to a number of common concerns regarding cognitive load which arise when using programming exercises in introductory physics classes where many students are absolute beginner programmers. This “hybrid” approach provides the student with a highly interactive web-based visualization, not unlike a PhET or Physlet interactive, but importantly the student is shown only the subset of the code where the initial conditions are set and the system variables are evolved. We highlight results from a coding activity that resembles the classic game Asteroids. The goals of this activity are to show how a simple 1D code can be modified into a 2D code, and to reinforce ideas about the relationship between force, velocity, and acceleration vectors. Survey results from four semesters of introductory physics classes at the Ohio State University's Marion campus, in which a high percentage of the students are weak or absolute beginner programmers, provide evidence that most students can complete coding tasks without severe difficulty. Other survey results are promising for future work where conceptual learning will be assessed in a direct way using metrics like the Animated Force Concept Inventory [Dancy and Beichner, Phys. Rev. Spec. Top. Phys. Educ. 2, 010104 (2006)]. The exercise highlighted here and others from our group are available for general use at http://compadre.org/PICUP.

Exploring DrugBank in Virtual Reality Chemical Space.

The recent general availability of low-cost virtual reality headsets and accompanying three-dimensional (3D) engine support presents an opportunity to bring the concept of chemical space into virtual environments. While virtual reality applications represent a category of widespread tools in other fields, their use in the visualization and exploration of abstract data such as chemical spaces has been experimental. In our previous work, we established the concept of interactive two-dimensional (2D) maps of chemical spaces followed by interactive web-based 3D visualizations, culminating in the interactive web-based 3D visualization of extremely large chemical spaces. Virtual reality chemical spaces are a natural extension of these concepts. As 2D and 3D embeddings and projections of high-dimensional chemical fingerprint spaces have been shown to be valuable tools in chemical space visualization and exploration, existing pipelines of data mining and preparation can be extended to be used in virtual reality applications. Here we present an application based on the Unity engine and the Virtual Reality Toolkit, allowing for the interactive exploration of chemical space populated by DrugBank compounds in virtual reality. The source code of the application as well as the most recent build are available on GitHub ( https://github.com/reymond-group/virtual-reality-chemical-space ).

Interactive web-based identification and visualization of transcript shared sequences

We have developed TraC (Transcript Consensus), a web-based tool for detecting and visualizing shared sequences among two or more mRNA transcripts such as splice variants. Results including exon-exon boundaries are returned in a highly intuitive, data-rich, interactive plot that permits users to explore the similarities and differences of multiple transcript sequences. The online tool (http://labs.pathology.jhu.edu/nauen/trac/) is free to use. The source code is freely available for download (https://github.com/nauenlab/TraC).

Weather Data Visualization and Analytical Platform

This article aims to present a web-based interactive visualization and analytical platform for weather data in Armenia by integrating the three existing infrastructures for observational data, numerical weather prediction, and satellite image processing. The weather data used in the platform consists of near-surface atmospheric elements including air temperature, pressure, relative humidity, wind and precipitation. The visualization and analytical platform has been implemented for 2-m surface temperature. The platform gives Armenian State Hydrometeorological and Monitoring Service analytical capabilities to analyze the in-situ observations, model and satellite image data per station and region for a given period.

FMLC: fast multi-level clustering and visualization of large molecular datasets.

Despite successful applications of data clustering and visualization techniques in molecular sequence identification, current technologies still do not scale to large biological datasets. We address this problem by a new multi-threaded tool, fMLC, primarily developed to cluster DNA sequences, that is supplemented with an interactive web-based visualization component, DiVE. fMLC enabled to compare, cluster and visualize 350K ITS fungal sequences at the species level. It took less than two hours to compare and cluster the dataset, which is twelve times faster than the time reported previously. https://github.com/FastMLC/fMLC (doi: 10.5281/zenodo.926820). d.vu@westerdijkinstitute.nl or v.robert@westerdijkinstitute.nl.

BioVis Explorer: A visual guide for biological data visualization techniques

Data visualization is of increasing importance in the Biosciences. During the past 15 years, a great number of novel methods and tools for the visualization of biological data have been developed and published in various journals and conference proceedings. As a consequence, keeping an overview of state-of-the-art visualization research has become increasingly challenging for both biology researchers and visualization researchers. To address this challenge, we have reviewed visualization research especially performed for the Biosciences and created an interactive web-based visualization tool, the BioVis Explorer. BioVis Explorer allows the exploration of published visualization methods in interactive and intuitive ways, including faceted browsing and associations with related methods. The tool is publicly available online and has been designed as community-based system which allows users to add their works easily.

Visual analytics and remote sensing imagery to support community-based research for precision agriculture in emerging areas

Agriculture in northern Ontario, Canada, has not yet reached the level of development of the southern regions of the province. In spite of the increasing desirability of the former region for agricultural expansion, northern agricultural producers – as well as other producers in “emerging” areas – have less access to information and decision support services relative to more established agricultural regions. At the same time, geographic information systems (GIS) are now being integrated into precision agriculture to assess field variability, to ensure optimal use of information, to maximize output, and to increase efficiency. To address this trend, a community-based research initiative based on an interactive web-based information visualization and GIS decision support system has been deployed with the aim of providing northern Ontario producers with access to the data they need to make the best possible decisions concerning their crops. This system employs citizen science and community-based participatory research to build a mutually beneficial partnership between agricultural producers, researchers, and other community stakeholders.

ENIGMA-Viewer: interactive visualization strategies for conveying effect sizes in meta-analysis

BackgroundGlobal scale brain research collaborations such as the ENIGMA (Enhancing Neuro Imaging Genetics through Meta Analysis) consortium are beginning to collect data in large quantity and to conduct meta-analyses using uniformed protocols. It becomes strategically important that the results can be communicated among brain scientists effectively. Traditional graphs and charts failed to convey the complex shapes of brain structures which are essential to the understanding of the result statistics from the analyses. These problems could be addressed using interactive visualization strategies that can link those statistics with brain structures in order to provide a better interface to understand brain research results.ResultsWe present ENIGMA-Viewer, an interactive web-based visualization tool for brain scientists to compare statistics such as effect sizes from meta-analysis results on standardized ROIs (regions-of-interest) across multiple studies. The tool incorporates visualization design principles such as focus+context and visual data fusion to enable users to better understand the statistics on brain structures. To demonstrate the usability of the tool, three examples using recent research data are discussed via case studies.ConclusionsENIGMA-Viewer supports presentations and communications of brain research results through effective visualization designs. By linking visualizations of both statistics and structures, users can gain more insights into the presented data that are otherwise difficult to obtain. ENIGMA-Viewer is an open-source tool, the source code and sample data are publicly accessible through the NITRC website (http://www.nitrc.org/projects/enigmaviewer_20). The tool can also be directly accessed online (http://enigma-viewer.org).

WebGIVI: a web-based gene enrichment analysis and visualization tool

BackgroundA major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined for enriched biological concepts. One approach to help the researcher interpret large gene datasets is to associate genes and informative terms (iTerm) that are obtained from the biomedical literature using the eGIFT text-mining system. However, examining large lists of iTerm and gene pairs is a daunting task.ResultsWe have developed WebGIVI, an interactive web-based visualization tool (http://raven.anr.udel.edu/webgivi/) to explore gene:iTerm pairs. WebGIVI was built via Cytoscape and Data Driven Document JavaScript libraries and can be used to relate genes to iTerms and then visualize gene and iTerm pairs. WebGIVI can accept a gene list that is used to retrieve the gene symbols and corresponding iTerm list. This list can be submitted to visualize the gene iTerm pairs using two distinct methods: a Concept Map or a Cytoscape Network Map. In addition, WebGIVI also supports uploading and visualization of any two-column tab separated data.ConclusionsWebGIVI provides an interactive and integrated network graph of gene and iTerms that allows filtering, sorting, and grouping, which can aid biologists in developing hypothesis based on the input gene lists. In addition, WebGIVI can visualize hundreds of nodes and generate a high-resolution image that is important for most of research publications. The source code can be freely downloaded at https://github.com/sunliang3361/WebGIVI. The WebGIVI tutorial is available at http://raven.anr.udel.edu/webgivi/tutorial.php.

SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.

SummaryAnalysis of HIV-1 virions from participants infected in a randomized controlled preventive HIV-1 vaccine efficacy trial can help elucidate mechanisms of partial protection. By comparing the genetic sequence of viruses from vaccine and placebo recipients to the sequence of the vaccine itself, a technique called ‘sieve analysis’, one can identify functional specificities of vaccine-induced immune responses. We have created an interactive web-based visualization and data access tool for exploring the results of sieve analyses performed on four major preventive HIV-1 vaccine efficacy trials: (i) the HIV Vaccine Trial Network (HVTN) 502/Step trial, (ii) the RV144/Thai trial, (iii) the HVTN 503/Phambili trial and (iv) the HVTN 505 trial. The tool acts simultaneously as a platform for rapid reinterpretation of sieve effects and as a portal for organizing and sharing the viral sequence data. Access to these valuable datasets also enables the development of novel methodology for future sieve analyses.Availability and ImplementationVisualization: http://sieve.fredhutch.org/viz. Source code: https://github.com/nkullman/SIEVE. Data API: http://sieve.fredhutch.org/data.