RCircos: an R package for Circos 2D track plots.
RCircos: an R package for Circos 2D track plots.
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RCIRCOS：Circos 2D轨道图的R包。
DOI：
10.1186/1471-2105-14-244
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发表时间：
2013-08-10
影响因子：
3
通讯作者：
Davis S
中科院分区：
文献类型：
--
作者：
Zhang H;Meltzer P;Davis S
Circos是基于Perl语言的软件包，用于可视化基因组结构的相似性和差异以及基因组间隔之间的位置关系。运行Circos需要额外的数据处理过程来准备绘图数据文件和从数据集配置文件，这限制了它与其他软件工具（如R）直接集成的能力。最近发布的R Bioconductor软件包ggbio提供了一个功能，可以基于多个其他软件包以圆形布局显示基因组数据，这增加了其使用的复杂性，并降低了与其他R管道集成的灵活性。我们实现了一个R包RCircos，只使用R基础安装附带的R包。该软件包支持Circos 2D数据跟踪图，如散点图、直线图、直方图、热图、平铺图、连接器、链接和文本标签。每个图都是用一个特定的函数实现的，所有函数的输入数据都是数据帧，可以是从文本文件中读取的对象，也可以是用其他R管道生成的对象。RCircos软件包提供了一种简单灵活的方法来使用R绘制Circos 2D轨迹图，并且可以很容易地集成到其他R数据处理和图形操作管道中，以呈现大规模多样本基因组研究数据。它也可以作为生成复杂Circos图像的基础工具。
Circos is a Perl language based software package for visualizing similarities and differences of genome structure and positional relationships between genomic intervals. Running Circos requires extra data processing procedures to prepare plot data files and configure files from datasets, which limits its capability of integrating directly with other software tools such as R. Recently published R Bioconductor package ggbio provides a function to display genomic data in circular layout based on multiple other packages, which increases its complexity of usage and decreased the flexibility in integrating with other R pipelines. We implemented an R package, RCircos, using only R packages that come with R base installation. The package supports Circos 2D data track plots such as scatter, line, histogram, heatmap, tile, connectors, links, and text labels. Each plot is implemented with a specific function and input data for all functions are data frames which can be objects read from text files or generated with other R pipelines. RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.