Code Cells: Knitr

Knitr is an R package for dynamic document generation. Learn more about using Knitr with Quarto in the article on Running Code.

Overview

Cell options affect the execution and output of executable code blocks. They are specified within comments at the top of a block. For example:

```{r}
#| label: fig-polar
#| echo: false
#| fig-cap: "A line plot on a polar axis"
```

Attributes

label

Unique label for code cell. Used when other code needs to refer to the cell (e.g. for cross references fig-samples or tbl-summary)

classes

Classes to apply to cell container

Code Output

eval

Evaluate code cells (if false just echos the code into output).

echo

Include cell source code in rendered output. Specify fenced to include the cell delimiter as part of the output.

code-fold

Collapse code into an HTML <details> tag so the user can display it on-demand. Specify show to have the code initiallly visible.

code-summary

Summary text to use for code blocks collapsed using code-fold

code-overflow

Choose whether to scroll or wrap when code lines are too wide for their container.

code-line-numbers

Include line numbers in code block output.

lst-label

Unique label for code listing (used in cross references)

lst-cap

Caption for code listing

tidy

Whether to reformat R code.

tidy-opts

List of options to pass to tidy handler

collapse

Collapse all the source and output blocks from one code chunk into a single block

prompt

Whether to add the prompt characters in R code. See prompt and continue on the help page ?base::options. Note that adding prompts can make it difficult for readers to copy R code from the output, so prompt: false may be a better choice. This option may not work well when the engine is not R (#1274).

class-source

Class name(s) for source code blocks

attr-source

Attribute(s) for source code blocks

Cell Output

output

Include the results of executing the code in the output (specify asis to treat output as raw markdown with no enclosing containers).

warning

Including warnings in rendered output.

error

Include errors in the output (note that this implies that errors executing code will not halt processing of the document).

include

Catch all for preventing any output (code or results) from being included in output.

panel

Panel type for cell output (tabset, input, sidebar, fill, center)

message

Including messages in rendered output.

results

How to display text results. Note that this option only applies to normal text output (not warnings, messages, or errors). The possible values are as follows:

  • markup: Mark up text output with the appropriate environments depending on the output format. For example, if the text output is a character string "[1] 1 2 3", the actual output that knitr produces will be:

    ```
    [1] 1 2 3
    ```

    In this case, results: markup means to put the text output in fenced code blocks (```).

  • asis: Write text output as-is, i.e., write the raw text results directly into the output document without any markups.

    ```{r}
    #| results: asis
    cat("I'm raw **Markdown** content.\n")
    ```
  • hold: Hold all pieces of text output in a chunk and flush them to the end of the chunk.

  • hide (or false): Hide text output.

comment

Prefix to be added before each line of text output. By default, the text output is commented out by ##, so if readers want to copy and run the source code from the output document, they can select and copy everything from the chunk, since the text output is masked in comments (and will be ignored when running the copied text). Set comment: '' to remove the default ##.

class-output

Class name(s) for text/console output

attr-output

Attribute(s) for text/console output

class-warning

Class name(s) for warning output

attr-warning

Attribute(s) for warning output

class-message

Class name(s) for message output

attr-message

Attribute(s) for message output

class-error

Class name(s) for error output

attr-error

Attribute(s) for error output

Figures

fig-width

Default width for figures

fig-height

Default height for figures

fig-cap

Figure caption

fig-subcap

Figure subcaptions

fig-link

Hyperlink target for the figure

fig-align

Horizontal alignment for the figure (default, left, right, or center)

fig-alt

Alternative text to be used in the alt attribute of HTML images.

fig-env

LaTeX environment for figure output

fig-pos

LaTeX figure position arrangement to be used in \begin{figure}[].

fig-scap

A short caption (only used in LaTeX output). A short caption is inserted in \caption[], and usually displayed in the “List of Figures” of a PDF document.

fig-format

Default output format for figures (retina, png, jpeg, svg, or pdf)

fig-dpi

Default DPI for figures

out-width

Width of the plot in the output document, which can be different from its physical fig-width, i.e., plots can be scaled in the output document. Depending on the output format, this option can take special values. For example, for LaTeX output, it can be .8\\linewidth, 3in, or 8cm; for HTML, it can be 300px.

out-height

Height of the plot in the output document, which can be different from its physical fig-height, i.e., plots can be scaled in the output document. Depending on the output format, this option can take special values. For example, for LaTeX output, it can be 3in, or 8cm; for HTML, it can be 300px.

fig-keep

How plots in chunks should be kept. Possible values are as follows:

  • high: Only keep high-level plots (merge low-level changes into high-level plots).
  • none: Discard all plots.
  • all: Keep all plots (low-level plot changes may produce new plots).
  • first: Only keep the first plot.
  • last: Only keep the last plot.
  • If set to a numeric vector, the values are indices of (low-level) plots to keep.
fig-show

How to show/arrange the plots. Possible values are as follows:

  • asis: Show plots exactly in places where they were generated (as if the code were run in an R terminal).
  • hold: Hold all plots and output them at the end of a code chunk.
  • animate: Concatenate all plots into an animation if there are multiple plots in a chunk.
  • hide: Generate plot files but hide them in the output document.
out-extra

Additional raw LaTeX or HTML options to be applied to figures

external

Externalize tikz graphics (pre-compile to PDF)

sanitize

sanitize tikz graphics (escape special LaTeX characters).

interval

Time interval (number of seconds) between animation frames.

aniopts

Extra options for animations; see the documentation of the LaTeX animate package.

animation-hook

Hook function to create animations in HTML output.

The default hook (ffmpeg) uses FFmpeg to convert images to a WebM video.

Another hook function is gifski based on the gifski package to create GIF animations.

Tables

tbl-cap

Table caption

tbl-subcap

Table subcaptions

tbl-colwidths

Apply explicit table column widths for markdown grid tables and pipe tables that are more than columns characters wide (72 by default).

Some formats (e.g. HTML) do an excellent job automatically sizing table columns and so don’t benefit much from column width specifications. Other formats (e.g. LaTeX) require table column sizes in order to correctly flow longer cell content (this is a major reason why tables > 72 columns wide are assigned explicit widths by Pandoc).

This can be specified as:

  • auto: Apply markdown table column widths except when there is a hyperlink in the table (which tends to throw off automatic calculation of column widths based on the markdown text width of cells). (auto is the default for HTML output formats)

  • true: Always apply markdown table widths (true is the default for all non-HTML formats)

  • false: Never apply markdown table widths.

  • [40,30,30]: Array of explicit width percentages.

Panel Layout

layout

2d-array of widths where the first dimension specifies columns and the second rows.

For example, to layout the first two output blocks side-by-side on the top with the third block spanning the full width below, use [[3,3], [1]].

Use negative values to create margin. For example, to create space between the output blocks in the top row of the previous example, use [[3,-1, 3], [1]].

layout-ncol

Layout output blocks into columns

layout-nrow

Layout output blocks into rows

layout-align

Horizontal alignment for layout content (default, left, right, or center)

layout-valign

Vertical alignment for layout content (default, top, center, or bottom)

Page Columns

column

Page column for output

fig-column

Page column for figure output

tbl-column

Page column for table output

cap-location

Where to place figure and table captions (top, bottom, or margin)

fig-cap-location

Where to place figure captions (top, bottom, or margin)

tbl-cap-location

Where to place table captions (top, bottom, or margin)

Cache

cache

Whether to cache a code chunk. When evaluating code chunks for the second time, the cached chunks are skipped (unless they have been modified), but the objects created in these chunks are loaded from previously saved databases (.rdb and .rdx files), and these files are saved when a chunk is evaluated for the first time, or when cached files are not found (e.g., you may have removed them by hand). Note that the filename consists of the chunk label with an MD5 digest of the R code and chunk options of the code chunk, which means any changes in the chunk will produce a different MD5 digest, and hence invalidate the cache.

cache-path

A prefix to be used to generate the paths of cache files

cache-vars

Variable names to be saved in the cache database. By default, all variables created in the current chunks are identified and saved, but you may want to manually specify the variables to be saved, because the automatic detection of variables may not be robust, or you may want to save only a subset of variables.

cache-globals

Variables names that are not created from the current chunk.

This option is mainly for autodep: true to work more precisely—a chunk B depends on chunk A when any of B’s global variables are A’s local variables. In case the automatic detection of global variables in a chunk fails, you may manually specify the names of global variables via this option. In addition, cache-globals: false means detecting all variables in a code chunk, no matter if they are global or local variables.

cache-lazy

Whether to lazyLoad() or directly load() objects. For very large objects, lazyloading may not work, so cache-lazy: false may be desirable (see #572).

cache-rebuild

Force rebuild of cache for chunk

cache-comments

Prevent comment changes from invalidating the cache for a chunk

dependson

Explicitly specify cache dependencies for this chunk (one or more chunk labels)

autodep

Detect cache dependencies automatically via usage of global variables

Include

child

One or more paths of child documents to be knitted and input into the main document.

file

File containing code to execute for this chunk

code

String containing code to execute for this chunk

purl

Include chunk when extracting code with knitr::purl()