Plotgardener: cultivating precise multi-panel figures in R
Plotgardener: cultivating precise multi-panel figures in R
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DOI：
10.1093/bioinformatics/btac057
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发表时间：
2022-02-04
期刊：
影响因子：
5.8
通讯作者：
Phanstiel, Douglas H.
中科院分区：
文献类型：
--
作者：
Kramer, Nicole E.;Davis, Eric S.;Phanstiel, Douglas H.
动机：R 编程语言是最广泛使用的编程语言之一，用于通过分析和可视化将原始基因组数据集转换为有意义的生物学结论，这在很大程度上得益于 Bioconductor 项目开发的基础设施和工具。然而，现有的绘图包依赖于图的相对定位和大小，这通常足以进行探索性分析，但不太适合创建科学手稿准备所固有的出版质量的多面板图像。结果：我们提出了plotgardener，一个基于坐标的基因组数据可视化包，它为 R 中的多图图形生成提供了新的范例。Plotgardener 允许对图的放置、美观和排列进行精确的编程控制，同时通过快速和灵活的方式最大限度地提高用户体验。内存高效的数据访问，支持多种数据和文件类型，以及与 Bioconductor 环境的紧密集成。 Plotgardener 还允许精确放置 ggplot2 绘图并调整其大小，这使其成为几乎任何学科的 R 用户和数据科学家的宝贵工具。
Motivation: The R programming language is one of the most widely used programming languages for transforming raw genomic datasets into meaningful biological conclusions through analysis and visualization, which has been largely facilitated by infrastructure and tools developed by the Bioconductor project. However, existing plotting packages rely on relative positioning and sizing of plots, which is often sufficient for exploratory analysis but is poorly suited for the creation of publication-quality multi-panel images inherent to scientific manuscript preparation.Results: We present plotgardener, a coordinate-based genomic data visualization package that offers a new paradigm for multi-plot figure generation in R. Plotgardener allows precise, programmatic control over the placement, esthetics and arrangements of plots while maximizing user experience through fast and memory-efficient data access, support for a wide variety of data and file types, and tight integration with the Bioconductor environment. Plotgardener also allows precise placement and sizing of ggplot2 plots, making it an invaluable tool for R users and data scientists from virtually any discipline.