The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
Bioinformatics. 2013 Aug 1;29(15):1890-2. doi: 10.1093/bioinformatics/btt294. Epub 2013 Jun 6.
Drawing genomic features in attractive and informative ways is a key task in visualization of genomics data. Scalable Vector Graphics (SVG) format is a modern and flexible open standard that provides advanced features including modular graphic design, advanced web interactivity and animation within a suitable client. SVGs do not suffer from loss of image quality on re-scaling and provide the ability to edit individual elements of a graphic on the whole object level independent of the whole image. These features make SVG a potentially useful format for the preparation of publication quality figures including genomic objects such as genes or sequencing coverage and for web applications that require rich user-interaction with the graphical elements.
SVGenes is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface. The library implements a simple Page object that spaces and contains horizontal Track objects that in turn style, colour and positions features within them. Tracks are the level at which visual information is supplied providing the full styling capability of the SVG standard. Genomic entities like genes, transcripts and histograms are modelled in Glyph objects that are attached to a track and take advantage of SVG primitives to render the genomic features in a track as any of a selection of defined glyphs. The feature model within SVGenes is simple but flexible and not dependent on particular existing gene feature formats meaning graphics for any existing datasets can easily be created without need for conversion.
The library is provided as a Ruby Gem from https://rubygems.org/gems/bio-svgenes under the MIT license, and open source code is available at https://github.com/danmaclean/bioruby-svgenes also under the MIT License.
以吸引人且富有信息量的方式绘制基因组特征是基因组学数据可视化的关键任务。可伸缩矢量图形 (SVG) 格式是一种现代而灵活的开放标准，提供了高级功能，包括模块化图形设计、高级 Web 交互性和动画功能，且适用于合适的客户端。SVG 在重新缩放时不会损失图像质量，并提供了编辑整个图形中单个元素的能力，而无需编辑整个图像。这些功能使得 SVG 成为一种有潜力的格式，可用于准备出版质量的图形，包括基因组对象（如基因或测序覆盖），以及需要与图形元素进行丰富用户交互的 Web 应用程序。
SVGenes 是一个 Ruby 语言库，它使用 SVG 基本元素通过简单灵活的 Ruby 接口来呈现典型的基因组符号。该库实现了一个简单的 Page 对象，该对象包含水平的 Track 对象，而 Track 对象则依次对其内部的特征进行样式、颜色和位置设置。Track 是提供视觉信息的级别，提供了 SVG 标准的全部样式功能。像基因、转录本和直方图等基因组实体在 Glyph 对象中建模，该对象附加到一个 Track 上，并利用 SVG 基本元素来呈现 Track 中的基因组特征，作为定义的符号之一。SVGenes 中的特征模型简单但灵活，不依赖于特定的现有基因特征格式，这意味着可以轻松地为任何现有数据集创建图形，而无需进行转换。
该库作为 Ruby Gem 从 https://rubygems.org/gems/bio-svgenes 提供，许可证为 MIT 许可证，开源代码可从 https://github.com/danmaclean/bioruby-svgenes 获得，许可证同样为 MIT 许可证。
