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. 2022 Mar 28;38(7):2042-2045.
doi: 10.1093/bioinformatics/btac057.

Plotgardener: cultivating precise multi-panel figures in R

Nicole E Kramer  1 , Eric S Davis  1 , Craig D Wenger  2 , Erika M Deoudes  3 , Sarah M Parker  1 , Michael I Love  4   5 , Douglas H Phanstiel  1   3   6   7   8
Affiliations

Plotgardener: cultivating precise multi-panel figures in R

Nicole E Kramer et al. Bioinformatics. .

Abstract

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.

Availability and implementation: Package: https://bioconductor.org/packages/plotgardener, Code: https://github.com/PhanstielLab/plotgardener, Documentation: https://phanstiellab.github.io/plotgardener/.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Plotgardener uses a coordinate-based plotting system to size and arrange plots. (a) Blueprint outline of a multi-omic figure to be created with specified dimensions and placements on a defined page. (b) Multi-panel, multi-omic figure programmatically created with plotgardener using the sizing and placement coordinates from (a). The plotgardener functions used to create this figure include pageCreate, plotHicSquare, annoHeatmapLegend, plotGenes, annoGenomeLabel, plotIdeogram, plotHicTriangle, plotSignal and plotText. Code to reproduce this plot is included in the plotgardener package
See this image and copyright information in PMC

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