gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2.
gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2.
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DOI：
10.12688/f1000research.16409.2
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发表时间：
2018
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影响因子：
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通讯作者：
Maag JLV
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作者：
Maag JLV
将数据显示在解剖结构上是一种快速观察组织相关信息的便捷技术。然而，绘制组织是一项复杂的任务，需要解剖学和艺术方面的专业知识。虽然基于网络的应用程序可以在类型图上显示基因表达，但其他非遗传学学科缺乏类似的工具。此外，基于Web的工具通常缺乏与编程语言中的包相关联的模块化，例如R。这里我介绍gganatgraph，这是一个R包，用于基于ggplot2的图形语法和Expression Atlas中公开可用的类型图的组合来绘制模块化物种类型图。这种组合允许快速、简单、模块化和可重复地生成类型图。该工具仅使用一个命令和一个包含组织名称、组、颜色和值的数据框，使用户能够以所需的颜色、按变量分组或显示所需的值，例如所选组织的基因表达、药代动力学或细菌负荷，来可视化特定的人和鼠组织。Gganatram由5个高度注释的生物组成，即雄性/雌性人/小鼠，以及一个细胞类型图。它还包括来自动植物界的其他24种较少被注释的生物。我希望这个工具将被更广泛的生物科学界所使用。欢迎社区成员提交更多的地形图，这些地形图可以包含在包中。稳定版本的gganatgraph已经存放到神经导体上，开发版本可以在http：//gihub/jespermaag/gganatgraph上找到。在https://jespermaag.shinyapps.io/gganatogram/，上可以找到一个互动的gganatgraph应用程序，它允许非R用户创建类似图。
Displaying data onto anatomical structures is a convenient technique to quickly observe tissue related information. However, drawing tissues is a complex task that requires both expertise in anatomy and the arts. While web based applications exist for displaying gene expression on anatograms, other non-genetic disciplines lack similar tools. Moreover, web based tools often lack the modularity associated with packages in programming languages, such as R. Here I present gganatogram, an R package used to plot modular species anatograms based on a combination of the graphical grammar of ggplot2 and the publicly available anatograms from the Expression Atlas. This combination allows for quick and easy, modular, and reproducible generation of anatograms. Using only one command and a data frame with tissue name, group, colour, and value, this tool enables the user to visualise specific human and mouse tissues with desired colours, grouped by a variable, or displaying a desired value, such as gene-expression, pharmacokinetics, or bacterial load across selected tissues. gganatogram consists of 5 highly annotated organisms, male/female human/mouse, and a cell anatogram. It further consists of 24 other less annotated organisms from the animal and plant kingdom. I hope that this tool will be useful by the wider community in biological sciences. Community members are welcome to submit additional anatograms, which can be incorporated into the package. A stable version gganatogram has been deposited to neuroconductor, and a development version can be found on github/jespermaag/gganatogram. An interactive shiny app of gganatogram can be found on https://jespermaag.shinyapps.io/gganatogram/, which allows for non-R users to create anatograms.