Tutorial: Computation does not render plot to PDF

[CCRMaster]

Hello,

I have a problem with the sample code in the Computation tutorial in the Quarto Get Stated section.
I am running Quarto in VS Code Version: 1.74.2 on a MacBook Pro running MacOS Ventura 13.1.

The code computations.qmd runs fine in VS Code in the Quarto Preview and it also generates properly the HTML file with all the graphs and plots. The problem I have is when rendering to PDF.
Then everything apart from the last Plotly plot is OK. Instead of the Plotly plot I get two lines in the PDF with the following text:
Unable to display output for mime type(s): text/html
Unable to display output for mime type(s): text/html

If I run Quarto on computations.qmd in the macOS terminal I get the same error in the PDF file.
The terminal run is the following:
frode@Frodes-Bogart Quarto % quarto render computations.qmd --to pdf

Executing 'computations.ipynb'
Cell 1/3...Done
Cell 2/3...Done
Cell 3/3...Done

pandoc
to: latex
output-file: computations.tex
standalone: true
pdf-engine: xelatex
variables:
graphics: true
tables: true
default-image-extension: pdf

metadata
documentclass: scrartcl
classoption:
- DIV=11
- numbers=noendperiod
papersize: letter
header-includes:
- '\KOMAoption{captions}{tableheading}'
block-headings: true
title: Quarto Computations
jupyter: python3

running xelatex - 1
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode

running xelatex - 2
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode

Output created: computations.pdf

Running a check on Quarto and Quarto tools I get:

frode@Frodes-Bogart Quarto % quarto check

[✓] Checking Quarto installation......OK
Version: 1.2.280
Path: /Applications/quarto/bin

[✓] Checking basic markdown render....OK

[✓] Checking Python 3 installation....OK
Version: 3.10.6
Path: /usr/local/opt/[email protected]/bin/python3.10
Jupyter: 5.1.2
Kernels: python3, ir

[✓] Checking Jupyter engine render....OK

[✓] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.19

[✓] Checking Knitr engine render......OK

frode@Frodes-Bogart Quarto % quarto tools check
[✓] Inspecting tools

Tool Status Installed Latest
chromium Up to date 869685 869685
tinytex Up to date v2023.01 v2023.01

I have installed in Python 3 Jupyter, Matplotlib, Plotly and Pandas

I have also tried various renderers by adding

import plotly.io as pio
pio.renderers.default = "plotly_mimetype+notebook_connected"

or
pio.renderers.default = "notebook"

without that changing anything to the missing Plotly plot in the PDF output.

Does anybody know what is wrong? Am I missing something?

Best regards,
Frode

[cscheid]

Plotly output only works in HTML formats.

[CCRMaster]

Hi Carlos,

Many thanks for the reply. I had seen that when looking at Plotly but I had hoped that there would have been some post processing from HTML to PDF such as is described here:
https://plotly.com/python/v3/pdf-reports/

Best regards,
Frode

[mvf]

Just let the Python cell write an image file, then include it in the Markdown:

```{python}
%%capture
import plotly.express as px
df = px.data.iris()
fig = px.density_heatmap(df, x='sepal_width', y='sepal_length', marginal_x='rug', marginal_y='histogram')
fig.write_image('myfig.svg')
```
![](myfig.svg)

I'm using SVG with the typst and docx backends. PDF is also supported. See plotly docs for more info.

To keep plots interactive when rendering to HTML, you'll have to resort to conditional divs:

::: {.content-visible when-format="html"}
```{python}
fig
```
:::

::: {.content-visible unless-format="html"}
![](myfig.svg)
:::

Downside of these is that labels and captions need to be repeated for the HTML and non-HTML case.