i2dash: Creation of Flexible, Interactive, and Web-Based Dashboards for Visualization of Omics Data

Abstract

Data visualization and interactive data exploration are important aspects of illustrating complex concepts and results from analyses of omics data. A suitable visualization has to be intuitive and accessible. Web-based dashboards have become popular tools for the arrangement, consolidation, and display of such visualizations. However, the combination of automated data processing pipelines handling omics data and dynamically generated, interactive dashboards is poorly solved. Here, we present i2dash, an R package intended to encapsulate functionality for the programmatic creation of customized dashboards. It supports interactive and responsive (linked) visualizations across a set of predefined graphical layouts. i2dash addresses the needs of data analysts/software developers for a tool that is compatible and attachable to any R-based analysis pipeline, thereby fostering the separation of data visualization on one hand and data analysis tasks on the other hand. In addition, the generic design of i2dash enables the development of modular extensions for specific needs. As a proof of principle, we provide an extension of i2dash optimized for single-cell RNA sequencing analysis, supporting the creation of dashboards for the visualization needs of such experiments. Equipped with these features, i2dash is suitable for extensive use in large-scale sequencing/bioinformatics facilities. Along this line, we provide i2dash as a containerized solution, enabling a straightforward large-scale deployment and sharing of dashboards using cloud services. i2dash is freely available via the R package archive CRAN (https://CRAN.R-project.org/package=i2dash).

Interactive and Reproducible Workflows for Exploring and Modeling RNA‐seq Data with pcaExplorer, Ideal, and GeneTonic

“…The provided template includes in one single compiled document most of the usually employed summaries for such datasets. Alternatively, exporting the data under exploration as a generic container (a SummarizedExperiment) makes it amenable to further processing with many existing interoperable software in the Bioconductor ecosystem, including iSEE (Rue‐Albrecht et al., 2018) for flexible bespoke graphical representations, or i2dash (Ustjanzew et al., 2021) for easy deployment of dedicated dashboards.…”

“…The iterative nature of the analysis of such high‐dimensional data can be assisted by other web applications, whose role might be complementary to the one proposed by pcaExplorer, ideal, and GeneTonic. As an example, the i2dash R package (Ustjanzew et al., 2021) is an excellent option to programmatically create and deploy such dashboards, as these can be coupled as data products to the existing R‐based analysis pipelines. This usage makes i2dash suitable to be adopted in biostatistics/bioinformatics research facilities, reducing the effort to develop and deploy dedicated data products.…”

“…A desktop/laptop computer, with standard modern configuration, and an up-to-date operating system. readers interested in exploring single-cell RNA-seq datasets are encouraged to use the iSEE and i2dash packages for this purpose (Rue-Albrecht et al, 2018;Ustjanzew, Preussner, Bentsen, Kuenne, & Looso, 2021), as also included in the Suggestions for Further Analysis section. For an easier reproducibility of the results presented in Basic Protocols 1 to 3, we prepared the data to be directly used in the protocols.…”