GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.
GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications.
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DOI：
10.1093/bioinformatics/btv376
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发表时间：
2015-10-15
期刊：
影响因子：
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通讯作者：
Brinkman FS
中科院分区：
文献类型：
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作者：
Laird MR;Langille MG;Brinkman FS
动机：基因组和相关元数据的简单静态图像是非常有限的，因为研究人员期望类似于后Web 2.0世界中的Web应用程序的丰富的交互式工具。GenomeD 3 Plot是一个轻量级的可视化库，使用D3库用JavaScript编写。GenomeD 3 Plot提供了丰富的API，允许使用方便的基于标准的JSON配置文件快速可视化复杂的基因组数据。当集成到现有的Web服务中时，GenomeD 3 Plot允许研究人员与数据交互，动态更改视图，甚至在浏览器窗口中调整或重新定位可视化。此外，GenomeD 3 Plot还内置了以PNG或SVG格式导出任何结果基因组可视化的功能，以便轻松包含在手稿或演示文稿中。结果如下：GenomeD 3 Plot被用于最近发布的Islandviewer 3（www.pathogenomics.sfu.ca/islandviewer/），以可视化预测的基因组岛与其他基因组注释数据。然而，它的功能使其能够更广泛地适用于一般的基因组数据的动态可视化。可用性和实施：GenomeD 3 Plot在https://github.com/brinkmanlab/GenomeD3Plot/上根据GNU-GPL v3许可。联系人：brinkman@sfu.ca
Motivation: A simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations. Results: GenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general. Availability and implementation: GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/. Contact: brinkman@sfu.ca