Visualizing dimensionality reduction of systems biology data

One of the challenges in analyzing high-dimensional expression data is the detection of important biological signals. A common approach is to apply a dimension reduction method, such as principal component analysis. Typically, after application of such a method the data is projected and visualized in the new coordinate system, using scatter plots or profile plots. These methods provide good results if the data have certain properties which become visible in the new coordinate system and which were hard to detect in the original coordinate system. Often however, the application of only one method does not suffice to capture all important signals. Therefore several methods addressing different aspects of the data need to be applied. We have developed a framework for linear and non-linear dimension reduction methods within our visual analytics pipeline SpRay. This includes measures that assist the interpretation of the factorization result. Different visualizations of these measures can be combined with functional annotations that support the interpretation of the results. We show an application to high-resolution time series microarray data in the antibiotic-producing organism Streptomyces coelicolor as well as to microarray data measuring expression of cells with normal karyotype and cells with trisomies of human chromosomes 13 and 21

Visual and interactive exploration of point data

Point data, such as Unit Postcodes (UPC), can provide very detailed information at fine scales of resolution. For instance, socio-economic attributes are commonly assigned to UPC. Hence, they can be represented as points and observable at the postcode level. Using UPC as a common field allows the concatenation of variables from disparate data sources that can potentially support sophisticated spatial analysis. However, visualising UPC in urban areas has at least three limitations. First, at small scales UPC occurrences can be very dense making their visualisation as points difficult. On the other hand, patterns in the associated attribute values are often hardly recognisable at large scales. Secondly, UPC can be used as a common field to allow the concatenation of highly multivariate data sets with an associated postcode. Finally, socio-economic variables assigned to UPC (such as the ones used here) can be non-Normal in their distributions as a result of a large presence of zero values and high variances which constrain their analysis using traditional statistics. This paper discusses a Point Visualisation Tool (PVT), a proof-of-concept system developed to visually explore point data. Various well-known visualisation techniques were implemented to enable their interactive and dynamic interrogation. PVT provides multiple representations of point data to facilitate the understanding of the relations between attributes or variables as well as their spatial characteristics. Brushing between alternative views is used to link several representations of a single attribute, as well as to simultaneously explore more than one variable. PVT’s functionality shows how the use of visual techniques embedded in an interactive environment enable the exploration of large amounts of multivariate point data

Coordinating views for data visualisation and algorithmic profiling

A number of researchers have designed visualisation systems that consist of multiple components, through which data and interaction commands flow. Such multistage (hybrid) models can be used to reduce algorithmic complexity, and to open up intermediate stages of algorithms for inspection and steering. In this paper, we present work on aiding the developer and the user of such algorithms through the application of interactive visualisation techniques. We present a set of tools designed to profile the performance of other visualisation components, and provide further functionality for the exploration of high dimensional data sets. Case studies are provided, illustrating the application of the profiling modules to a number of data sets. Through this work we are exploring ways in which techniques traditionally used to prepare for visualisation runs, and to retrospectively analyse them, can find new uses within the context of a multi-component visualisation system

VIOLA - A multi-purpose and web-based visualization tool for neuronal-network simulation output

Neuronal network models and corresponding computer simulations are invaluable tools to aid the interpretation of the relationship between neuron properties, connectivity and measured activity in cortical tissue. Spatiotemporal patterns of activity propagating across the cortical surface as observed experimentally can for example be described by neuronal network models with layered geometry and distance-dependent connectivity. The interpretation of the resulting stream of multi-modal and multi-dimensional simulation data calls for integrating interactive visualization steps into existing simulation-analysis workflows. Here, we present a set of interactive visualization concepts called views for the visual analysis of activity data in topological network models, and a corresponding reference implementation VIOLA (VIsualization Of Layer Activity). The software is a lightweight, open-source, web-based and platform-independent application combining and adapting modern interactive visualization paradigms, such as coordinated multiple views, for massively parallel neurophysiological data. For a use-case demonstration we consider spiking activity data of a two-population, layered point-neuron network model subject to a spatially confined excitation originating from an external population. With the multiple coordinated views, an explorative and qualitative assessment of the spatiotemporal features of neuronal activity can be performed upfront of a detailed quantitative data analysis of specific aspects of the data. Furthermore, ongoing efforts including the European Human Brain Project aim at providing online user portals for integrated model development, simulation, analysis and provenance tracking, wherein interactive visual analysis tools are one component. Browser-compatible, web-technology based solutions are therefore required. Within this scope, with VIOLA we provide a first prototype.Comment: 38 pages, 10 figures, 3 table

Bubble-Wall Plot: A New Tool for Data Visualization

This research aimed to design a new tool for data visualization with performed features - named Bubble-Wall Plot and assumed that it could be an effective tool for developing data visualization systems. This research reviewed seven data visualization approaches for identifying the outliers, including Line Charts, Parallel Coordinates Plot, Scatter Plots, TreeMap, Glyphs, Pixel-based techniques, and Redial visualizations. The challenges for current data visualization approaches were also summarized. Two principles were addressed to design the new tool- keep it simple strategy with the smallest strategy. As a result, the newly designed Bubble-Wall Plot has successfully been adopted to develop a warning system for identifying the outliers in a Case Study company, which was deployed for user acceptance testing in May 2021. The main contribution is that this newly designed tool with the simplest style was well-designed and proven to effectively develop a warning visualization system