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Free, publicly-accessible full text available May 11, 2025
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Abstract Background Direct-sequencing technologies, such as Oxford Nanopore’s, are delivering long RNA reads with great efficacy and convenience. These technologies afford an ability to detect post-transcriptional modifications at a single-molecule resolution, promising new insights into the functional roles of RNA. However, realizing this potential requires new tools to analyze and explore this type of data.
Result Here, we present Sequoia, a visual analytics tool that allows users to interactively explore nanopore sequences. Sequoia combines a Python-based backend with a multi-view visualization interface, enabling users to import raw nanopore sequencing data in a Fast5 format, cluster sequences based on electric-current similarities, and drill-down onto signals to identify properties of interest. We demonstrate the application of Sequoia by generating and analyzing ~ 500k reads from direct RNA sequencing data of human HeLa cell line. We focus on comparing signal features from m6A and m5C RNA modifications as the first step towards building automated classifiers. We show how, through iterative visual exploration and tuning of dimensionality reduction parameters, we can separate modified RNA sequences from their unmodified counterparts. We also document new, qualitative signal signatures that characterize these modifications from otherwise normal RNA bases, which we were able to discover from the visualization.
Conclusions Sequoia’s interactive features complement existing computational approaches in nanopore-based RNA workflows. The insights gleaned through visual analysis should help users in developing rationales, hypotheses, and insights into the dynamic nature of RNA. Sequoia is available at
https://github.com/dnonatar/Sequoia . -
Narrative visualization is a popular style of data-driven storytelling. Authors use this medium to engage viewers with complex and sometimes controversial issues. A challenge for authors is to not only deliver new information, but to also overcome people’s biases and misconceptions. We study how people adjust their attitudes toward (or away from) a message experienced through a narrative visualization. In a mixed-methods analysis, we investigate whether eliciting participants’ prior beliefs, and visualizing those beliefs alongside actual data, can increase narrative persuasiveness. We find that incorporating priors does not significantly affect attitudinal change. However, participants who externalized their beliefs expressed greater surprise at the data. Their comments also indicated a greater likelihood of acquiring new information, despite the minimal change in attitude. Our results also extend prior findings, showing that visualizations are more persuasive than equivalent textual data representations for exposing contentious issues. We discuss the implications and outline future research directions.more » « less
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Abstract Color encoding is foundational to visualizing quantitative data. Guidelines for colormap design have traditionally emphasized perceptual principles, such as order and uniformity. However, colors also evoke cognitive and linguistic associations whose role in data interpretation remains underexplored. We study how two linguistic factors, name salience and name variation, affect people's ability to draw inferences from spatial visualizations. In two experiments, we found that participants are better at interpreting visualizations when viewing colors with more salient names (e.g., prototypical ‘blue’, ‘yellow’, and ‘red’ over ‘teal’, ‘beige’, and ‘maroon’). The effect was robust across four visualization types, but was more pronounced in continuous (e.g., smooth geographical maps) than in similar discrete representations (e.g., choropleths). Participants' accuracy also improved as the number of nameable colors increased, although the latter had a less robust effect. Our findings suggest that color nameability is an important design consideration for quantitative colormaps, and may even outweigh traditional perceptual metrics. In particular, we found that the linguistic associations of color are a better predictor of performance than the perceptual properties of those colors. We discuss the implications and outline research opportunities. The data and materials for this study are available at
https://osf.io/asb7n -
We investigate how to co-opt the perception of causality to aid the analysis of multivariate data. We propose Dynamic Glyphs (DyGs), an animated extension to traditional glyphs. DyGs encode data relations through seemingly physical interactions between glyph parts. We hypothesize that this representation gives rise to impressions of causality, enabling observers to reason intuitively about complex, multivariate dynamics. In a crowdsourced experiment, participants’ accuracy with DyGs exceeded or was comparable to non-animated alternatives. Moreover, participants showed a propensity to infer higher-dimensional relations with DyGs. Our findings suggest that visual causality can be an effective ‘channel’ for communicating complex data relations that are otherwise difficult to think about. We discuss the implications and highlight future research opportunities.more » « less
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Data visualization provides a powerful way for analysts to explore and make data-driven discoveries. However, current visual analytic tools provide only limited support for hypothesis-driven inquiry, as their built-in interactions and workflows are primarily intended for exploratory analysis. Visualization tools notably lack capabilities that would allow users to visually and incrementally test the fit of their conceptual models and provisional hypotheses against the data. This imbalance could bias users to overly rely on exploratory analysis as the principal mode of inquiry, which can be detrimental to discovery. In this paper, we introduce Visual (dis) Confirmation, a tool for conducting confirmatory, hypothesis-driven analyses with visualizations. Users interact by framing hypotheses and data expectations in natural language. The system then selects conceptually relevant data features and automatically generates visualizations to validate the underlying expectations. Distinctively, the resulting visualizations also highlight places where one's mental model disagrees with the data, so as to stimulate reflection. The proposed tool represents a new class of interactive data systems capable of supporting confirmatory visual analysis, and responding more intelligently by spotlighting gaps between one's knowledge and the data. We describe the algorithmic techniques behind this workflow. We also demonstrate the utility of the tool through a case study.more » « less