Data Visualization

Fix Quarto Julia Plotly Bugs: 5 Essential Steps (2025)

Struggling with broken Plotly plots in your Quarto Julia documents? Learn 5 essential, up-to-date steps for 2025 to fix common bugs and render flawlessly.

Dr. Elena Petrova

Computational scientist and data visualization enthusiast specializing in Julia and reproducible research.

September 8, 20256 min read13 views

You’ve done it. You’ve wrangled your data in Julia, crafted the perfect interactive visualization with Plotly, and it looks absolutely stunning in your VS Code plot pane. Now, the final step: rendering your Quarto document to share your masterpiece with the world. You run quarto render, open the HTML file, and... nothing. Just a gaping blank space where your beautiful plot should be. Or maybe it’s a mangled, tiny version of your chart, completely unusable.

If this sounds familiar, you're not alone. The combination of Quarto, Julia, and Plotly is incredibly powerful for creating reproducible, interactive reports, but a few common gotchas can turn a smooth workflow into a frustrating debugging session. The good news is that most of these issues stem from a handful of simple misunderstandings about how these tools talk to each other.

Forget tearing your hair out. We’re going to walk through the five most essential steps to diagnose and fix virtually any issue you'll encounter with Julia-based Plotly plots in Quarto for 2025. Let's get your visualizations back on track.

Step 1: Tame the Environment Mismatch

This is, without a doubt, the most common culprit. The Julia environment your interactive session (like in a Jupyter notebook or the VS Code REPL) is using might not be the same one Quarto uses when it renders your document. Quarto starts a fresh Julia session for rendering, and if it doesn't know about your project's specific dependencies, it won't be able to find packages like PlotlyJS.jl.

The result? A cryptic error in your render log, or more often, a silent failure where the plot just doesn't appear.

The Fix: Explicitly Activate Your Project

The most robust solution is to tell Quarto exactly which environment to use. Add this snippet to the very first Julia code chunk in your .qmd document:

# In your first Julia code chunk
using Pkg
# Assumes Project.toml is in the same directory as your .qmd file
Pkg.activate(".")

This command forces Quarto’s Julia process to use the Project.toml and Manifest.toml files in your project directory, ensuring it has access to the exact same package versions you used during development. No more guessing games.

Step 2: Master Quarto's Display Logic

In an interactive Julia session, you're used to the last object in a cell being automatically displayed. Quarto, however, is a bit more formal. It needs to be explicitly told what to output from a code chunk. If you create a plot object but then perform another action, Quarto might not render the plot you intended.

The Fix: Make Your Plot the Last Expression

The rule of thumb is simple: the object you want to display must be the very last thing evaluated in the code chunk.

Consider this common mistake:

# --- This might NOT render in Quarto --- 
using PlotlyJS

function create_plot()
    p = plot(rand(10, 2), Layout(title="My Data"))
    return p
end

my_plot = create_plot()
some_other_variable = 42 # This is the last expression, so '42' is returned, not the plot!

Quarto sees 42 as the output of this chunk and displays nothing. The fix is to ensure your plot object is the final line:

# --- This WILL render correctly --- 
using PlotlyJS

function create_plot()
    p = plot(rand(10, 2), Layout(title="My Data"))
    return p
end

some_other_variable = 42
my_plot = create_plot() # Now the plot object is the last expression

Alternatively, you can be even more explicit by using display(), which can be helpful in more complex scripts or loops. However, simply making the plot object the last line is the most idiomatic approach.

Step 3: Get Your YAML Header Right

The YAML header (the part at the top of your .qmd file between ---) is Quarto’s control panel. A single misconfiguration here can prevent Plotly’s JavaScript library from being loaded correctly, leaving you with a blank canvas.

Think of the YAML header as the instruction manual you give to Quarto before it starts building your document. If the instructions are wrong, the result will be too.

The Fix: Ensure Resource Embedding

For creating portable, single-file HTML reports, one setting is paramount: embed-resources. This tells Quarto to bundle all necessary assets—like the Plotly.js library—directly into your HTML file.

Here’s a robust starter YAML header for a Julia and Plotly project:

---
title: "Interactive Julia Report"
author: "Dr. Elena Petrova"
format:
  html:
    embed-resources: true
    theme: cosmo
engine: julia
---

Without embed-resources: true, the browser might fail to fetch the Plotly JavaScript library, especially when you view the file offline or send it to a colleague. This simple line solves a world of headaches.

Step 4: Clarify the PlotlyJS Backend

This is a more subtle issue, but it can be a real showstopper. PlotlyJS.jl is smart and tries to guess the best way to show a plot based on the environment it's in (e.g., a browser, the VS Code plot pane, a terminal). Sometimes, its guess during a Quarto render can be wrong.

You can see this if your plot renders, but interactivity is broken, or if it tries to open a new browser tab instead of embedding the plot in your document.

The Fix: Set the Display Mode Manually

You can give PlotlyJS.jl a hint about where it's being rendered. While the default :auto mode has improved significantly, explicitly setting it can provide a more stable rendering experience.

Add this line right after you import PlotlyJS:

using PlotlyJS

# Help PlotlyJS understand it's in an environment that needs embedded HTML
PlotlyJS.set_display_mode!(:auto)

In recent versions, :auto is quite reliable for Quarto. It correctly detects that it should output the necessary HTML and JavaScript for embedding. If you ever face strange rendering artifacts, knowing this command exists is your secret weapon.

Step 5: Adopt a Bulletproof Debugging Workflow

When the four steps above don't solve your problem, it's time to stop guessing and start investigating systematically. A solid debugging workflow will save you hours of frustration.

The Fix: Isolate, Inspect, and Interrogate

Follow this three-pronged approach to hunt down any remaining bugs.

Tactic	What It Does	Why It Helps
Isolate the Problem	Create a new, minimal `.qmd` file with only the code for the broken plot.	This immediately tells you if the issue is with the plot code itself or a conflict with another part of your document.
Inspect the Logs	Render from the terminal with verbose logging: `quarto render your-doc.qmd --log-level DEBUG`	This prints every step Quarto takes. Search the output for "ERROR", "WARNING", or "Julia" to find hidden error messages from the Julia engine.
Interrogate the Output	Add `keep-html: true` to your YAML header and render. Then, open the resulting HTML file in a browser and use the Developer Tools (F12).	Check the 'Console' tab for JavaScript errors. Is there a "Plotly is not defined" error? This points to a resource-embedding problem (Step 3).

Wrapping Up: Your Path to Flawless Plots

The synergy between Julia's analytical power, Plotly's interactivity, and Quarto's publishing elegance is a game-changer for technical communication. While the occasional rendering hiccup can be discouraging, it's almost always traceable to one of these five areas:

Environment: Make sure Quarto uses your project's Julia environment.
Display Logic: Ensure your plot object is the last expression in its chunk.
YAML Config: Embed your resources for self-contained, reliable reports.
Backend Hinting: Gently guide PlotlyJS on how to render.
Debugging: Isolate, inspect, and interrogate when all else fails.

By internalizing these checks, you'll transform from a frustrated debugger into a confident creator. You'll spend less time fighting with your tools and more time building the insightful, beautiful, and interactive documents that your work deserves.

Have another go-to trick for debugging Quarto plots? Share your wisdom in the comments below!