Flexible Linked Axes for Multivariate Data Visualization

In this work, we present an effective and scalable system for multivariate volume data visualization and analysis with a novel Transfer Function (TF) interface design that tightly couples parallel coordinates plots (PCP) and MDS-based dimension projection plots. In our system, the PCP visualizes the data distribution of each variate and the MDS plots project features. Together, they are integrated seamlessly to provide flexible feature classification without context switching between different data presentations during the user interaction. The proposed interface enables users to identify relevant correlation clusters and assign optical properties on them. To further support large scale multivariate volume data visualization and analysis, we develop three integrated parallel systems to accelerate the rendering of PCP, the layout of MDS, as well as parallel rendering of multivarite volume data. Our experiments show that the system is effective in multivariate volume data visualization and its performance is scalable for data sets with different sizes and number of variates.

Over the past decades, parallel coordinates plots (PCPs) have been extensively applied to various tasks of multivariate data visualization. However, a main disadvantage of PCPs is the almost inevitable overlap of polylines, which causes chaotic visual effects when the number of polylines is large and the sequence of parallel coordinates is not conducive to visualization. To tackle this issue, this paper proposed an axis permutation of PCPs based on Laplacian scores (LS), which can be used to enhance the visualization performance of the original PCPs. The enhanced PCP is a combination of an unsupervised feature selection technique (LS) and the visualization of multivariate data. With the new sequence of axes based on the Laplacian scores of the corresponding features, polylines of PCPs are distributed with less clutter and overlap. The experimental results demonstrated that the proposed method made great progress in enhancing the visualization performance of PCPs.

This paper proposes a dynamic analytical processing (DAP) visualization tool based on the Bubble-Wall Plot. It can be handily used to develop visual warning systems for visualizing the dynamic analytical processes of hazard data. Comparative analysis and case study methods are used in this research. Based on a literature review of Q1 publications since 2017, 23 types of data visualization approaches/tools are identified, including seven anomaly data visualization tools. This study presents three significant findings by comparing existing data visualization approaches. The primary finding is that no single visualization tool can fully satisfy industry requirements. This finding motivates academics to develop new DAP visualization tools. The second finding is that there are different views of Line Charts and various perspectives on Scatter Plots. The other one is that different researchers may perceive an existing data visualization tool differently, such as arguments between Scatter Plots and Line Charts and diverse opinions about Parallel Coordinate Plots and Scatter Plots. Users' awareness rises when they choose data visualization tools that satisfy their requirements. By conducting a comparative analysis based on five categories (Style, Value, Change, Correlation, and Others) with 26 subcategories of metric features, results show that this new tool can effectively solve the limitations of existing visualization tools as it appears to have three remarkable characteristics: the simplest cartographic tool, the most straightforward visual result, and the most intuitive tool. Furthermore, this paper illustrates how the Bubble-Wall Plot can be effectively applied to develop a warning system for presenting dynamic analytical processes of hazard data in the coal mine. Lastly, this paper provides two recommendations, one implication, six research limitations, and eleven further study topics.

This paper describes an R package which produces tours of multivariate data. The package includes functions for creating different types of tours, including grand, guided, and little tours, which project multivariate data (p-D) down to 1, 2, 3, or, more generally, d (≤ p) dimensions. The projected data can be rendered as densities or histograms, scatterplots, anaglyphs, glyphs, scatterplot matrices, parallel coordinate plots, time series or images, and viewed using an R graphics device, passed to GGobi, or saved to disk. A tour path can be stored for visualisation or replay. With this package it is possible to quickly experiment with different, and new, approaches to tours of data. This paper contains animations that can be viewed using the Adobe Acrobat PDF viewer.

Ribosomal profiling is an emerging experimental technology to measure protein synthesis by sequencing short mRNA fragments undergoing translation in ribosomes. Applied on the genome wide scale, this is a powerful tool to profile global protein synthesis within cell populations of interest. Such information can be utilized for biomarker discovery and detection of treatment-responsive genes. However, analysis of ribosomal profiling data requires careful preprocessing to reduce the impact of artifacts and dedicated statistical methods for visualizing and modeling the high-dimensional discrete read count data. Here we present Ribosomal Profiling Reports (RP-REP), a new open-source cloud-enabled software that allows users to execute start-to-end gene-level ribosomal profiling and RNA-Seq analysis on a pre-configured Amazon Virtual Machine Image (AMI) hosted on AWS or on the user’s own Ubuntu Linux server. The software works with FASTQ files stored locally, on AWS S3, or at the Sequence Read Archive (SRA). RP-REP automatically executes a series of customizable steps including filtering of contaminant RNA, enrichment of true ribosomal footprints, reference alignment and gene translation quantification, gene body coverage, CRAM compression, reference alignment QC, data normalization, multivariate data visualization, identification of differentially translated genes, and generation of heatmaps, co-translated gene clusters, enriched pathways, and other custom visualizations. RP-REP provides functionality to contrast RNA-SEQ and ribosomal profiling results, and calculates translational efficiency per gene. The software outputs a PDF report and publication-ready table and figure files. As a use case, we provide RP-REP results for a dengue virus study that tested cytosol and endoplasmic reticulum cellular fractions of human Huh7 cells pre-infection and at 6 h, 12 h, 24 h, and 40 h post-infection. Case study results, Ubuntu installation scripts, and the most recent RP-REP source code are accessible at GitHub. The cloud-ready AMI is available at AWS (AMI ID: RPREP RSEQREP (Ribosome Profiling and RNA-Seq Reports) v2.1 (ami-00b92f52d763145d3)).

Much attention has been focused on the provision of information graphics and visualisations inside a web browser.Currently available infovis toolkits produce graphical output by either injecting SVG nodes into the DOM orusing the JavaScript Canvas 2D API. FluidDiagrams is a prototype information visualisation framework writtenin JavaScript which uses the WebGL 3D JavaScript API for its output, falling back to Canvas 2D as necessary,via the Three.js library. Six visualisations are currently implemented: bar chart and line chart, scatter plot andparallel coordinates for multidimensional data, and cone tree and hyperbolic for hierarchies.Anecdotally, visualisations using SVG nodes in the DOM for output can become rather sluggish when displayingmore than a few dozen items. Visualisations using Canvas 2D exhibit similarly slow performance. WebGLutilises hardware acceleration where available and promises much better performance for complex visualisations,potentially in the order of many thousands of items without becoming unresponsive.A comparison of parallel coordinates visualisations with 100 records in 20 dimensions compared three implementations:FluidDiagrams (WebGL), FluidDiagrams (Canvas 2D), and D3 (using SVG nodes). They achieved62, 6, and 10 frames per second respectively. The FluidDiagrams (WebGL) implementation was able to render1,000 records in 20 dimensions at 18 frames per second, compared to 1 and 6 respectively

Many graphical methods for displaying multivariate data consist of arrangements of multiple displays of one or two variables; scatterplot matrices and parallel coordinates plots are two such methods. In principle these methods generalize to arbitrary numbers of variables but become difficult to interpret for even moderate numbers of variables. This article demonstrates that the impact of high dimensions is much less severe when the component displays are clustered together according to some index of merit. Effectively, this clustering reduces the dimensionality and makes interpretation easier. For scatterplot matrices and parallel coordinates plots clustering of component displays is achieved by finding suitable permutations of the variables. I discuss algorithms based on cluster analysis for finding permutations, and present examples using various indices of merit.

Although simple and based on physical realizable color primaries, the RGB color space cannot allow the direct definition of a topology-preserving, perceptually-compatible inter-color distance. The classical normalized inter-color distances are rather complex to implement and tune. We propose the use of a planar color representation plot, derived from multivariate data visualization using parallel coordinates, which allows the introduction of a luminance-invariant, geometry-based inter-color distance. We show that the new distance is used with good results in the implementation of distance-based color filters and edge detectors.

The first step is to analyze the statistical graphics in use, so we examine the descriptive statistics. Next is the boxplot, the Q-Q plot, the histogram, the regressogram, the barchart, the dotchart, the piechart, the 2D-scatterplot, the 2D-contour plot, the scatterplot matrix, the 3D-scatterplot, the 3D-contour plot, the Chernoff faces and the parallel coordinate plot. We use some of the tools of XploRe to examine the Berlin housing dataset which use the plots mentioned above. Finally we state that two kinds of windows are necessary, one which can draw points, lines and areas, another which can draw glyphs windows, i.e. the Chernoff faces, star diagrams and so on.

The vdmR package generates web-based visual data mining tools by adding interactive functions to ggplot2 graphics. Brushing and linking between multiple plots is one of the main features of this package. Currently, scatter plots, histograms, parallel coordinate plots, and choropleth maps are supported in the vdmR package. In addition, identification on a plot is supported by linking the plot and the data table.

Traditional multidimensional visualization techniques, such as glyphs, parallel coordinates and scatterplot matrices, suffer from clutter at the display level and difficult user navigation among dimensions when visualizing high dimensional datasets. In this paper, we propose a new multidimensional visualization technique named a value and relation (VaR) display, together with a rich set of navigation and selection tools, for interactive exploration of datasets with up to hundreds of dimensions. By explicitly conveying the relationships among the dimensions of a high dimensional dataset, the VaR display helps users grasp the associations among dimensions. By using pixel-oriented techniques to present values of the data items in a condensed manner, the VaR display reveals data patterns in the dataset using as little screen space as possible. The navigation and selection tools enable users to interactively reduce clutter, navigate within the dimension space, and examine data value details within context effectively and efficiently. The VaR display scales well to datasets with large numbers of data items by employing sampling and texture mapping. A case study on a real dataset, as well as the VaR displays of multiple real datasets throughout the paper, reveals how our proposed approach helps users interactively explore high dimensional datasets with large numbers of data items

We explore how to rigorously evaluate multidimensional visualizations for their ability to support decision making. We first define multi-attribute choice tasks, a type of decision task commonly performed with such visualizations. We then identify which of the existing multidimensional visualizations are compatible with such tasks, and set out to evaluate three elementary visualizations: parallel coordinates, scatterplot matrices and tabular visualizations. Our method consists in first giving participants low-level analytic tasks, in order to ensure that they properly understood the visualizations and their interactions. Participants are then given multi-attribute choice tasks consisting of choosing holiday packages. We assess decision support through multiple objective and subjective metrics, including a decision accuracy metric based on the consistency between the choice made and self-reported preferences for attributes. We found the three visualizations to be comparable on most metrics, with a slight advantage for tabular visualizations. In particular, tabular visualizations allow participants to reach decisions faster. Thus, although decision time is typically not central in assessing decision support, it can be used as a tie-breaker when visualizations achieve similar decision accuracy. Our results also suggest that indirect methods for assessing choice confidence may allow to better distinguish between visualizations than direct ones. We finally discuss the limitations of our methods and directions for future work, such as the need for more sensitive metrics of decision support.

Multidimensional projections are an increasingly popular technique for visualizing large datasets containing observations having tens or even hundreds of dimensions. Compared to other techniques such as parallel coordinates, tables, and scatterplot matrices, they support tasks such as finding groups of related observations and outliers in simpler, more effective, ways. The authors discuss here the advantages of multidimensional projections, how to compute them, and recent advances that enhance them by visual explanatory techniques, so as to make them efficient and effective instruments that should be part of the toolkit of any scientist interested in high-dimensional data exploration.

Discovering and extracting linear trends and correlations in datasets is very important for analysts to understand multivariate phenomena. However, current widely used multivariate visualization techniques, such as parallel coordinates and scatterplot matrices, fail to reveal and illustrate such linear relationships intuitively, especially when more than 3 variables are involved or multiple trends coexist in the dataset. We present a novel multivariate model parameter space visualization system that helps analysts discover single and multiple linear patterns and extract subsets of data that fit a model well. Using this system, analysts are able to explore and navigate in model parameter space, interactively select and tune patterns, and refine the model for accuracy using computational techniques. We build connections between model space and data space visually, allowing analysts to employ their domain knowledge during exploration to better interpret the patterns they discover and their validity. Case studies with real datasets are used to investigate the effectiveness of the visualizations.

Patterns of metastasis and nodal disease in tongue and buccal carcinomas: Case-based reflections in Delhi NCR Region.