shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics
shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics
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DOI：
10.1371/journal.pone.0176334
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发表时间：
2017-05-11
期刊：
影响因子：
3.7
通讯作者：
Wahlestedt, Claes
中科院分区：
文献类型：
--
作者：
Khomtchouk, Bohdan B.;Hennessy, James R.;Wahlestedt, Claes
背景
转录组学、代谢组学、宏基因组学以及其他各种新一代测序（组学）领域因其产生大量数据集而闻名，特别是在单细胞测序研究中。对如此大数据进行可视化在生物学领域带来了技术挑战，无论是在可用计算资源方面，还是在编程能力方面。由于热图用于将高维数值数据描绘为彩色单元格网格，在成功将数据转换为图形的过程中，效率和速度往往被证明是关键考虑因素。例如，从大型输入数据集（例如10万行以上）绘制交互式热图在台式计算机和网络浏览器上在计算上都是不可行的。除了内存要求外，编程技能和知识经常是创建高度可定制热图的准入障碍。
结果
我们提出了shinyheatmap：一个先进的、用户友好的热图软件套件，能够在网络浏览器中高效地创建高度可定制的静态和交互式生物热图。shinyheatmap是一个内存占用低的程序，这使其特别适合对由于大小限制通常无法在内存中计算的超大型数据集进行交互式可视化。此外，shinyheatmap具有一个内置的高性能网络插件fastheatmap，用于在几秒内快速绘制多达10⁵ - 10⁷行数据集的交互式热图，有效地打破了之前热图绘制速度的性能基准。
结论
shinyheatmap作为一个具有直观图形用户界面的免费网络服务器在线托管：http://shinyheatmap.com。这些方法在R语言中实现，并作为shinyheatmap项目的一部分在以下网址提供：https://github.com/Bohdan - Khomtchouk/shinyheatmap。用户可以从shinyheatmap网络界面内部直接访问fastheatmap，并且所有源代码已在Github上公开：https://github.com/Bohdan - Khomtchouk/fastheatmap。
BackgroundTranscriptomics, metabolomics, metagenomics, and other various next-generation sequencing (-omics) fields are known for their production of large datasets, especially across single-cell sequencing studies. Visualizing such big data has posed technical challenges in biology, both in terms of available computational resources as well as programming acumen. Since heatmaps are used to depict high-dimensional numerical data as a colored grid of cells, efficiency and speed have often proven to be critical considerations in the process of successfully converting data into graphics. For example, rendering interactive heatmaps from large input datasets (e.g., 100k+ rows) has been computationally infeasible on both desktop computers and web browsers. In addition to memory requirements, programming skills and knowledge have frequently been barriers-to-entry for creating highly customizable heatmaps.ResultsWe propose shinyheatmap: an advanced user-friendly heatmap software suite capable of efficiently creating highly customizable static and interactive biological heatmaps in a web browser. shinyheatmap is a low memory footprint program, making it particularly well-suited for the interactive visualization of extremely large datasets that cannot typically be computed in-memory due to size restrictions. Also, shinyheatmap features a built-in high performance web plug-in, fastheatmap, for rapidly plotting interactive heatmaps of datasets as large as 10(5)-10(7) rows within seconds, effectively shattering previous performance benchmarks of heatmap rendering speed.Conclusionsshinyheatmap is hosted online as a freely available web server with an intuitive graphical user interface: http://shinyheatmap.com. The methods are implemented in R, and are available as part of the shinyheatmap project at: https://github.com/Bohdan-Khomtchouk/ shinyheatmap. Users can access fastheatmap directly from within the shinyheatmap web interface, and all source code has been made publicly available on Github: https://github.com/Bohdan-Khomtchouk/fastheatmap.