+
+
+
+
+
The Plotgardener App interface is divided into three regions: the
+Panel List, the Parameters Panel, and
+the Figure Preview. The Panel List on
+the left provides icon-based navigation between four sections —
+Page, Plots, Save,
+and Code. The Parameters Panel in the
+center displays the relevant controls for whichever section is active.
+The Figure Preview on the right shows a live rendering
+of your figure. This guide walks through each section and describes a
+typical workflow for building a figure from start to finish.
+
+
+
The Page Tab
+
+
Before adding any plots, use the Page tab to set the
+overall canvas dimensions for your figure. Its settings appear in the
+Parameters Panel.
+
Settings available:
+
+-
+Width / Height: Physical dimensions of the output
+figure (in the selected units).
+-
+Units: Choose from inches (
in),
+centimeters (cm), or millimeters (mm).
+-
+Default parameters: Set package-wide defaults —
+such as genome assembly or font size — that apply across all panels
+unless overridden at the panel level.
+
+
Once you have configured the page, click Run Script
+to render a blank page in the Figure Preview. Page
+dimensions directly determine the size of the exported PDF. If you are
+targeting a specific journal figure size (e.g., single-column = 3.5 in,
+double-column = 7 in), set those here.
+
For more on how the plotgardener coordinate system
+works, see The plotgardener
+Page.
+
+
+
The Plots Tab
+
+
The Plots tab is where you add, configure, and
+arrange individual visualization panels. Select it from the
+Panel List to load its controls into the
+Parameters Panel.
+
+
Adding a Panel
+
+
+- Select a
plotgardener function from the
+Function dropdown in the Parameters
+Panel. All functions supported by the installed version of
+plotgardener are listed automatically.
+- Give the panel a descriptive name in the Panel Name
+field.
+- Upload your data file using the Browse button next
+to the relevant data parameter.
+- Fill in the required parameters (clearly labeled in the interface).
+Optional parameters can be left at their defaults.
+- Click Add Plot to place the panel on the page.
+- Click Run Script to render the updated figure in
+the Figure Preview.
+
+
+
+
Editing a Panel
+
+
Select any existing panel from the Panel List,
+adjust its parameters in the Parameters Panel, and
+click Update Plot, then Run Script to
+re-render.
+
+
+
Adding Annotations
+
+
To layer annotations onto an existing panel (e.g., a highlight box,
+genome axis, or domain boundary), select the target panel from the
+Panel List, then choose an annotation function from the
+Annotations dropdown and configure its parameters. See
+Plot Annotations for details on available
+annotation types.
+
+
+
+
The app accepts the same data formats as the
+plotgardener R package:
+
+
+
+
+
+
+
+
+plotSignal |
+
+.bigWig, .bw
+ |
+
+
+
+plotHicSquare, plotHicRectangle,
+plotHicTriangle
+ |
+
+.hic, .cool, .mcool
+ |
+
+
+
+plotGenes, plotTranscripts
+ |
+Bioconductor annotation packages (e.g., TxDb.*) |
+
+
+
+plotPairs, plotPairsArches
+ |
+.bedpe |
+
+
+plotRanges |
+
+.bed, .narrowPeak,
+.broadPeak
+ |
+
+
+plotManhattan |
+Data frame with chrom, pos, p
+columns |
+
+
+
+
For a full description of data formats and how to prepare your files,
+see Reading Data for
+plotgardener.
+
+
+
+
The Save Tab
+
+
The Save tab lets you preserve and restore your
+entire figure session. Select it from the Panel List to
+access its controls in the Parameters Panel.
+
+-
+Save Session: Exports the current configuration —
+all panels, parameter values, and page settings — as a structured
+
.json file.
+-
+Load Session: Imports a previously saved
+
.json file to restore a figure exactly as it was, including
+all panels and their parameter values.
+
+
Sessions are portable across machines, making it straightforward to
+share figure templates with collaborators or reproduce figures in a
+different environment.
+
+
+
The Code Tab
+
+
The Code tab displays the R script that the app
+generates from your current panel configuration. Select it from the
+Panel List to view the script in the Parameters
+Panel.
+
+- The script updates in real time as you add, remove, or modify
+panels.
+- Click Copy to copy the full script to your
+clipboard and paste it into RStudio or any other IDE.
+- Advanced users can use this script as a starting point for
+customization beyond what the GUI supports — adding custom color
+palettes, looping over multiple regions, or integrating with other
+Bioconductor objects.
+
+
This tab is particularly useful for learning: configure a plot in the
+Plots tab, then switch to Code to
+inspect the equivalent plotgardener R function calls.
+
+
+
Typical Workflow
+
+
A complete figure-building session follows this sequence:
+
+-
+Set the page — Select the Page tab
+from the Panel List, enter your figure dimensions and
+units in the Parameters Panel, and click Run
+Script.
+-
+Add your first panel — Select the
+Plots tab, choose a function, upload your data, and
+enter the genomic coordinates (chromosome, start, end) and any required
+parameters.
+-
+Preview the figure — Click Run
+Script. The Figure Preview on the right
+renders the current figure.
+-
+Add more panels — Repeat steps 2–3 for each
+additional track or panel, positioning them on the page using the x, y,
+width, and height parameters.
+-
+Add annotations — Layer genome axis labels,
+highlight regions, domain boundaries, or other annotations onto existing
+panels.
+-
+Save your session — Select the
+Save tab and export the session as a
.json
+file for later use or sharing.
+-
+Export the R script — Select the
+Code tab and copy the generated script for archiving,
+further customization, or reproducibility.
+
+
+
+