Code Cells

Code Cells

Quarto uses a hashpipe (#|) syntax for code cell options, providing a clean, YAML-based approach that works across R, Python, Julia, and other languages.

Hashpipe Syntax

Code cell options are specified with #| at the start of lines within the code block:

```{r}
#| label: fig-scatter
#| echo: false
#| fig-cap: "A scatter plot of x versus y."
#| fig-width: 8
#| fig-height: 6

plot(x, y)
```

```{python}
#| label: fig-histogram
#| fig-cap: "Distribution of values."

import matplotlib.pyplot as plt
plt.hist(data)
plt.show()
```

Important: Options use dashes, not dots. Use fig-cap not fig.cap, fig-width not fig.width.

Execution Options

Control whether and how code is executed:

Examples

Show code but don't run it:

```{r}
#| eval: false

# This code is displayed but not executed
x <- 1 + 1
```

Run code but hide it:

```{r}
#| echo: false

# This code runs but is not shown
library(ggplot2)
```

Show fenced code block with attributes:

```{r}
#| echo: fenced

plot(1:10)
```

Figure Options

Options for controlling figure output:

Figure Example

```{r}
#| label: fig-analysis
#| fig-cap: "Analysis results showing the relationship between variables."
#| fig-alt: "Scatter plot with trend line showing positive correlation."
#| fig-width: 10
#| fig-height: 6
#| fig-align: center

ggplot(data, aes(x, y)) +
  geom_point() +
  geom_smooth()
```

Multiple Figures

```{r}
#| label: fig-panels
#| fig-cap: "Multiple panel figure."
#| fig-subcap:
#|   - "Distribution of X"
#|   - "Distribution of Y"
#| layout-ncol: 2

hist(x)
hist(y)
```

Table Options

Options for controlling table output:

Table Example

```{r}
#| label: tbl-summary
#| tbl-cap: "Summary statistics by group."

knitr::kable(summary_data)
```

Caching and Freeze

Control caching of code cell results:

Caching Example

```{r}
#| label: slow-computation
#| cache: true

# This expensive computation is cached
result <- slow_function(data)
```

Project-Level Freeze

In _quarto.yml:

execute:
  freeze: auto # Re-render only when source changes

Document-Level Defaults

Set defaults for all code cells in YAML front matter:

title: "My Document"
execute:
  echo: false
  warning: false
  message: false

Or per-format:

format:
  html:
    code-fold: true
  pdf:
    echo: false

Code Display Options

Control how code is displayed in HTML output:

Code Folding

In YAML front matter:

format:
  html:
    code-fold: true
    code-summary: "Click to see code"

Per cell override:

```{r}
#| code-fold: show

# This code is visible by default
plot(1:10)
```

Code Annotations

Add annotations to explain code:

```{r}
#| code-annotations: hover

library(tidyverse)
mtcars |>                 # <1>
  filter(mpg > 20) |>     # <2>
  select(mpg, cyl, hp)    # <3>
```

1. Start with the mtcars dataset
2. Filter to cars with MPG over 20
3. Select only the columns we need

Annotation styles: hover, select, below, beside.

Filename Display

Show a filename above the code block:

```{python}
#| filename: "analysis.py"

import pandas as pd
df = pd.read_csv("data.csv")
```

R Markdown Migration

R Markdown uses dots (.), Quarto uses dashes (-): fig.cap → fig-cap, fig.width → fig-width. Options move from chunk header to #| lines. results="asis" becomes output: asis. Setup chunks with knitr::opts_chunk$set(...) become execute: in YAML. See conversion-rmarkdown.md for full details.

Resources

• Quarto Code Cells
• Quarto Figures
• Code Annotation