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SVGenes: a library for rendering genomic features in scalable vector graphic format

机译:SVGenes:一个以可伸缩矢量图形格式呈现基因组特征的库

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摘要

>Motivation: 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.>Results: 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.>Availability: The library is provided as a Ruby Gem from under the MIT license, and open source code is available at also under the MIT License.>Contact:
机译:>动机:以有吸引力的信息方式绘制基因组特征是基因组数据可视化的关键任务。可伸缩矢量图形(SVG)格式是一种现代且灵活的开放标准,可在合适的客户端中提供高级功能,包括模块化图形设计,高级Web交互性和动画。 SVG不会因重新缩放而损失图像质量,并且可以在整个对象级别上独立于整个图像来编辑图形的各个元素。这些功能使SVG成为潜在的有用格式,可用于准备包括基因或基因序列等基因组对象的出版物质量数据,以及需要用户与图形元素进行丰富交互的Web应用程序。>结果:一个使用SVG原语通过简单灵活的Ruby界面呈现典型基因组字形的Ruby语言库。该库实现了一个简单的Page对象,该对象间隔并包含水平Track对象,这些对象依次具有样式,颜色和位置特征。轨道是提供视觉信息的级别,可提供SVG标准的完整样式功能。基因组实体(如基因,转录本和直方图)在附加到轨道上的字形对象中建模,并利用SVG原语将轨迹中的基因组特征呈现为任意定义的字形。 SVGenes中的特征模型简单但灵活,并且不依赖于特定的现有基因特征格式,这意味着无需转换即可轻松创建任何现有数据集的图形。>可用性:该库以Ruby Gem的形式提供可以从MIT许可证中获得,并且也可以从MIT许可证中获得开源代码。>联系方式:

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