# 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.

- Skill: `tools-only/code-cells` (Agent Skill, multi-file: 3 files)
- Install (CLI): `npx skillmds@latest add tools-only/code-cells`
- Raw SKILL.md: https://api.skillmd.com/api/skills/tools-only/code-cells/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: tools-only (https://skillmd.com/u/tools-only)
- Updated: 2026-09-29
- Page: https://skillmd.com/skills/tools-only/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:

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

plot(x, y)
```
````

````markdown
```{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:

| Option    | Description                               | Values                    |
| --------- | ----------------------------------------- | ------------------------- |
| `eval`    | Evaluate the code                         | `true`, `false`           |
| `echo`    | Include source code in output             | `true`, `false`, `fenced` |
| `output`  | Include results in output                 | `true`, `false`, `asis`   |
| `warning` | Include warnings                          | `true`, `false`           |
| `error`   | Include errors (stop on error if `false`) | `true`, `false`           |
| `include` | Include cell in output at all             | `true`, `false`           |

### Examples

Show code but don't run it:

````markdown
```{r}
#| eval: false

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

Run code but hide it:

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

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

Show fenced code block with attributes:

````markdown
```{r}
#| echo: fenced

plot(1:10)
```
````

## Figure Options

Options for controlling figure output:

| Option             | Description                      | Example                         |
| ------------------ | -------------------------------- | ------------------------------- |
| `fig-cap`          | Figure caption                   | `"A descriptive caption."`      |
| `fig-subcap`       | Subcaptions for multiple figures | `["Plot A", "Plot B"]`          |
| `fig-width`        | Width in inches                  | `8`                             |
| `fig-height`       | Height in inches                 | `6`                             |
| `fig-alt`          | Alt text for accessibility       | `"Scatter plot showing..."`     |
| `fig-align`        | Alignment                        | `"left"`, `"center"`, `"right"` |
| `fig-cap-location` | Caption position                 | `"top"`, `"bottom"`, `"margin"` |
| `fig-format`       | Output format                    | `"png"`, `"svg"`, `"pdf"`       |
| `fig-dpi`          | Resolution in DPI                | `300`                           |

### Figure Example

````markdown
```{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

````markdown
```{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:

| Option             | Description                     | Example                         |
| ------------------ | ------------------------------- | ------------------------------- |
| `tbl-cap`          | Table caption                   | `"Summary statistics."`         |
| `tbl-subcap`       | Subcaptions for multiple tables | `["Table A", "Table B"]`        |
| `tbl-colwidths`    | Column widths                   | `[40, 60]` or `"auto"`          |
| `tbl-cap-location` | Caption position                | `"top"`, `"bottom"`, `"margin"` |

### Table Example

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

knitr::kable(summary_data)
```
````

## Caching and Freeze

Control caching of code cell results:

| Option       | Description                         | Values                    |
| ------------ | ----------------------------------- | ------------------------- |
| `cache`      | Cache results                       | `true`, `false`           |
| `cache-lazy` | Use lazy loading for cached objects | `true`, `false`           |
| `freeze`     | Never re-render (project option)    | `true`, `false`, `"auto"` |

### Caching Example

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

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

### Project-Level Freeze

In `_quarto.yml`:

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

## Document-Level Defaults

Set defaults for all code cells in YAML front matter:

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

Or per-format:

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

## Code Display Options

Control how code is displayed in HTML output:

| Option              | Description          | Values                    |
| ------------------- | -------------------- | ------------------------- |
| `code-fold`         | Collapsible code     | `true`, `false`, `"show"` |
| `code-summary`      | Text for fold toggle | `"Show code"`             |
| `code-tools`        | Code tools menu      | `true`, `false`           |
| `code-line-numbers` | Show line numbers    | `true`, `false`           |
| `code-overflow`     | Handle overflow      | `"scroll"`, `"wrap"`      |

### Code Folding

In YAML front matter:

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

Per cell override:

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

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

## Code Annotations

Add annotations to explain code:

````markdown
```{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:

````markdown
```{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](conversion-rmarkdown.md) for full details.

## Resources

- [Quarto Code Cells](https://quarto.org/docs/computations/execution-options.html)
- [Quarto Figures](https://quarto.org/docs/authoring/figures.html)
- [Code Annotation](https://quarto.org/docs/authoring/code-annotation.html)