Getting Started with the Plotgardener App

Source: vignettes/guides/plotgardenerApp_getting_started.Rmd

What is the Plotgardener App?

plotgardener is an R/Bioconductor package for building flexible, multi-panel, publication-quality genomic visualizations. It has been downloaded over a thousand times and cited in over 100 papers, but using it requires proficiency in R, package management, and the command line. For many biologists, that can be a significant barrier.

The Plotgardener App is a desktop application that wraps the plotgardener R package in a graphical interface, making its full feature set available in a no-code environment. Users can add and configure Hi-C contact maps, signal tracks, gene models, genome labels, and more, all through point-and-click menus. A live rendering of the figure updates as you work, and at any point the app displays the underlying R script so that advanced users can copy and extend it further in any IDE.

A multipanel genomic figure built with the Plotgardener App, showing Hi-C contact maps, signal tracks, and gene models arranged on a single canvas.
A multipanel genomic figure built with the Plotgardener App, showing Hi-C contact maps, signal tracks, and gene models arranged on a single canvas.

Key Features

  • No-code visualization: Build multipanel genomic figures through point-and-click menus — no R required.
  • Live figure preview: See a rendered figure update in real time as you configure and add panels.
  • Code transparency: The app generates and displays the underlying R script at any point, enabling advanced users to copy, modify, and extend their figures in any IDE.
  • Dynamic interface: A built-in Python parser reads the live plotgardener R package source to automatically populate supported functions, parameters, and documentation — the interface stays synchronized with package updates without manual maintenance.
  • Session saving: Save and reload entire figure sessions as structured JSON files, enabling reusable templates and easy collaboration.

Platform Support

The Plotgardener App requires macOS (Apple Silicon M1/M2/M3 or Intel). Windows and Linux are not supported at this time. See Install the Plotgardener App for download and installation instructions.

Under the Hood

The Plotgardener App is built on Electron and comprises three layers:

  • Frontend (React): Renders all user-facing tabs and form elements, dynamically populated based on the selected plotgardener function.
  • Backend (Node.js): Manages all parameter inputs, maintains panel state across additions and edits, compiles the final R script, and returns the PDF output to the preview pane.
  • Parser (Python): Parses the live plotgardener R package source — functions, parameters, and documentation — into structured JSON. This keeps the interface automatically synchronized with any updates to the package, with no manual maintenance required.

Next Steps

Source Code