Publish and Share with Quarto :: Cheatsheet

QMD Edition

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Overview

¹

• Author: Write and code in plain text. Author documents as .qmd files, or Jupyter notebooks. Write in a rich Markdown syntax.

• Render: Generate documents, presentations and more. Produce HTML, PDF, MS Word, reveal.js, MS Powerpoint, Beamer, websites, blogs, books…

• Share: Share your work with the world. Quickly deploy to GitHub Pages, Netlify, Quarto Pub, Posit Cloud, or Posit Connect.

Get Quarto

Get Quarto from: https://quarto.org/docs/download/

Or, use version bundled with RStudio.

Get Started

https://quarto.org/docs/get-started

Author

Source File: hello.qmd

---
title: "Hello, Penguins"
format: html
execute:
  echo: false
---

## Meet the penguins

The `penguins` data contains size measurements for 
penguins from three islands in the Palmer Archipelago, 
Antarctica.

The three species of penguins have quite distinct 
distributions of physical dimensions (@fig-penguins).

```{r}
#| label: fig-penguins
#| fig-cap: "Dimensions of penguins across three species."
#| warning: false
library(tidyverse, quietly = TRUE)
library(palmerpenguins)
penguins |>
  ggplot(aes(x = flipper_length_mm, y = bill_length_mm)) +
  geom_point(aes(color = species)) +
  scale_color_manual(
    values = c("darkorange", "purple", "cyan4")) +
  theme_minimal()
```

Highlights in the source file

• Set format(s) and options. Use YAML Syntax.

  ---
  title: "Hello, Penguins"
  format: html
  execute:
    echo: false
  ---

• ## Write with **Markdown**

  RStudio: Help > Markdown Quick Reference

  RStudio & VS Code: Use the Visual Editor

  ## Meet the penguins
  
  The `penguins` data contains size measurements for 
  penguins from three islands in the Palmer Archipelago, 
  Antarctica.
  
  The three species of penguins have quite distinct 
  distributions of physical dimensions (@fig-penguins).

• Include code. R, Python, Julia, Observable, or any language with a Jupyter kernel.

  ```{r}
  #| label: fig-penguins
  #| fig-cap: "Dimensions of penguins across three species."
  #| warning: false
  library(tidyverse, quietly = TRUE)
  library(palmerpenguins)
  penguins |>
    ggplot(aes(x = flipper_length_mm, y = bill_length_mm)) +
    geom_point(aes(color = species)) +
    scale_color_manual(
      values = c("darkorange", "purple", "cyan4")) +
    theme_minimal()
  ```

Use a tool with a rich authoring experience

RStudio, or
Visual Studio Code + Quarto extension

• Run code cells as you write

• Render with a button or keyboard shortcut

• Edit Quarto documents with a Visual Editor

  

  • Apply formatting in Visual Editor. Saved as Markdown in source.

  • Insert elements like code cells, cross references, and more.

Or any text editor

Quarto documents (.qmd) can be edited in any tool that edits text.

Render

Save, then render to preview the document output.

Terminal

quarto preview hello.qmd

RStudio: Use Render button

VS Code: Use Preview button

The resulting HTML/PDF/MS Word/etc. document will be created and saved in the same directory as the source .qmd file.

Rendered output: hello.html

Highlights in the rendered output

• Features for scientific publishing. Cross references, citations, equations, and more.

• Output integrated into document. Control how output appears with special comments in your code.

Behind the Scenes

When you render a document, Quarto:

1. Runs the code and embeds results and text into an .md file with:
   • Knitr, if any {r} cells, or
   • Jupyter, if any other cells.
2. Converts the .md file into the output format with Pandoc.

Publish

Terminal

quarto publish {venue} hello.qmd

{venue}: quarto-pub, connect, gh-pages, netlify, confluence, posit-cloud

RStudio: Use Publish button

• Quarto Pub Free publishing service for Quarto content.

• Posit Cloud Cloud-hosted, control access to project and output.

• Posit Connect Org-hosted, control access, schedule updates.

Quarto Projects

Create websites, books and more

A directory of Quarto documents + a configuration file (_quarto.yml)

See examples at: https://quarto.org/docs/gallery/

Get started from the command line:

Terminal

quarto create project {type}

{type}: default, website, blog, book, confluence, manuscript

RStudio: Use File > New Project

Include Code

Code Cells

Code cells start with ```{language}, and end with ```.

RStudio & VS Code: Use Insert Code Chunk/Cell.

```{r}
#| label: chunk-id
```

```{python}
#| label: chunk-id
```

Other languages: {julia}, {ojs}

Add code cell options with #| comments.

Cell options control execution, figures, tables, layout and more. See them all at: https://quarto.org/docs/reference/cells/

Execution Options

Option	Default	Effects
echo	true	false: hide code in output fenced: include code cell syntax
eval	true	false: don’t run code
include	true	false: don’t include code or results
output	true	false: don’t include results asis: treat results as raw markdown
warning	true	false: don’t include warnings in output
error	false	true: include error in output and continue with render

Set execution options at the cell level:

```{r}
#| echo: false
```

```{python}
#| echo: false
```

Set options in code cells with #| comments and YAML syntax: key: value.

Or globally in the YAML header with the execute option:

---
execute:
  echo: false
---

Inline Code

Use computed values directly in text sections. Code is evaluated at render and results appear as text.

Knitr

Value is `r 2 + 2`.

Jupyter

Value is `{python} 2 + 2`.

Output

Value is 4.

Set Formats and Options

Set Format Options

---
title: "My Document"
format: 
  html: 
    code-fold: true
    toc: true
---

• Indent format 2 spaces
• Indent options 4 spaces

Multiple Formats

---
title: "My Document"
toc: true
format: 
  html: 
    code-fold: true
  pdf: default
---

• Top-level options (e.g. toc) apply to all formats

Common values for format: html, pdf², docx, odt, rtf, gfm, pptx, revealjs, beamer ³

Render all formats:

Terminal

quarto render hello.qmd

Render a specific format:

Terminal

quarto render hello.qmd --to pdf

Output Options Table

Important Options. The first column is the option name, an “X” in the next three columns indicates whether the option applies to the format, the fourth column decribes the options and possible values, the final column indicates whether the options can also be set in a code cell.

Option	html/revealjs	pdf/beamer	docx/pptx	Description	cell level?
Navigation
toc	X	X	X	Add a table of contents (true or false)
toc-depth	X	X	X	Lowest level of headings to add to table of contents (e.g. 2, 3)
anchor-sections	X			Show section anchors on mouse hover (true or false)
Style
highlight-style	X	X	X	Syntax highlighting theme (e.g. arrow, pygments, kate, zenburn)
mainfont, monofont	X	X		Font name. HTML: sets CSS font-family; LaTeX: via fontspec package
theme	X			Bootswatch theme name (e.g. cosmo, darkly, solar etc.)
css	X			CSS or SCSS file to use to style the document (e.g.
reference-doc			X	docx/pptx file containing template styles (e.g. file.docx, file.pptx)
NA
include-in-header	X	X		Files of content to include in header of output document, also include-before-body, include-after-body
keep-md	X	X	X	Keep intermediate files (true or false), also keep-tex, keep-ipynb
LaTeX
documentclass		X		LaTeX document class, set document options with classoption
pdf-engine		X		LaTeX engine to produce PDF output (xelatex, pdflatex, lualatex)
cite-method		X		Method used to format citations (citeproc, natbib, biblatex)
Code
code-fold	X			Let readers toggle the display of R code (false, true, or show)	X
code-tools	X			Add menu for hiding, showing, and downloading code (true or false)
code-overflow	X			Display of wide code (scroll, or wrap)	X
Figures
fig-align	X	X	docx only	Alignment of figures (default, left, right, center)	X
fig-width, fig-height	X	X	X	Default width and height for figures in inches	Knitr only
fig-format	X	X	X	Format for Matplotlib or R figures (retina, png, jpeg, svg, or pdf)

Visit https://quarto.org/docs/reference/ to see all options by format

Add Content

Figures

Markdown

![CAP](image.png){#fig-LABEL fig-alt="ALT"}

Computation

```{python}
#| label: fig-LABEL
#| fig-cap: CAP
#| fig-alt: ALT
{{ plot code here }}
```

Or {r}

Tables

Markdown

|object | radius|
|:------|------:|
|Sun    | 696000|
|Earth  |   6371|

: CAPTION {#tbl-LABEL}

Computation

Output a markdown table or an HTML table from your code.

Knitr

Use knitr::kable() to produce markdown:

```{r}
#| label: tbl-LABEL
#| tbl-cap: CAPTION

knitr::kable(head(cars))
```

Also see the R packages: gt, flextable, kableExtra.

Jupyter

Add Markdown() to Markdown output:

```{python}
#| label: tbl-LABEL
#| tbl-cap: CAPTION
import pandas as pd, tabulate
from IPython.display import Markdown
df = pd.DataFrame({"A": [1, 2], 
                   "B": [1, 2]})
Markdown(df.to_markdown(index=False))
```

Cross References

1. Add labels:

   • Code cell: add option label: prefix-LABEL
   • Markdown: add attribute #prefix-LABEL

2. Add references: @prefix-LABEL, e.g.

   You can see in @fig-scatterplot, that...

prefix	Renders
fig-	Figure 1
tbl-	Table 1
eq-	Equation 1
sec-	Section 1

Citations

1. Add bibliography file to the YAML header:

   ---
   bibliography: references.bib
   ---

2. Add citations: [@citation], or @citation

RStudio & VS Code: Use Insert Citations dialog in the Visual Editor. Build your bibliography file from your Zotero library, DOI, Crossref, DataCite, or PubMed.

Callouts

::: {.callout-tip}
## Title

Text
:::

Instead of tip use one of: note, caution, warning, or important:

tip

note

caution

warning

important

Shortcodes

{{< include _file.qmd >}}

{{< embed file.ipynb#id >}}

{{< video video.mp4 >}}

---

CC BY SA Posit Software, PBC • info@posit.co • posit.co

Learn more at quarto.org.

Quarto 1.4

Updated: 2024-05.

---

Footnotes

1. Artwork from “Hello, Quarto” keynote by Julia Lowndes and Mine Çetinkaya-Rundel, presented at RStudio Conference 2022. Illustrated by Allison Horst.

2. PDFs and Beamer slides require LaTeX, use:

   Terminal

   quarto install tinytex

3. PDFs and Beamer slides require LaTeX, use:

   Terminal

   quarto install tinytex