- 🎨 knitr hooks allow full control over R Markdown output styling, including message(), warning(), and print().
- 🖥 HTML output supports detailed styling with CSS, unlike PDF or Word where styles are limited or overridden.
- 💬 Reusable functions help apply consistent design across large reports, boosting maintainability.
- ⚠️ Inline HTML won’t render in PDF or Word outputs unless handled with LaTeX or specific formatting tweaks.
- 📘 chunk options allow visibility control, but hooks are essential for direct output styling.
R Markdown is a very useful tool in data science, reporting, and analysis work. While it lets you mix code, writing, and results easily, the standard look of messages, print outputs, and warnings often isn’t as polished as needed for professional papers or client talks. Changing how output looks using knitr’s hooks and HTML/CSS helps you make reports much easier to read, show what’s important, and match your team’s look. And it keeps R Markdown’s flexible nature.
Understanding knitr’s Rendering Pipeline
To change how output looks in R Markdown, you need to understand knitr. This package reads your R Markdown (.Rmd) files and turns them into reports. knitr processes code chunks and sends output based on what kind it is:
- Standard output (like from
print()) - Messages (usually from
message()) - Warnings and errors (from
warning()or errors when running code)
Each type is handled differently when the report is made.
- Standard outputs are caught by default and printed as text.
- Messages and warnings are stopped unless chunk options say not to (
message=FALSE,warning=FALSE). - Errors can stop the process or be caught, depending on how things are set up.
By default, knitr uses hooks to handle each output type. Hooks stop the output, letting you change how it looks before it goes in your final document. This lets you control exactly how text is styled, placed, or even hidden.
Default Styling Behavior in R Markdown
If you’ve made a report using R Markdown without adding any style, you probably saw that the output doesn’t look the best:
print()output uses a monospaced font.message()output is usually gray or slightly slanted in HTML.- In PDFs, LaTeX styling is used, which often makes them look the same.
- Word outputs remove most styles, showing both print output and messages as normal text.
While these standard styles are neutral and easy to read, they can make real reports harder to use. For example, if your report has important numbers and less important logs, readers can’t easily tell them apart without things like color or size.
Why Customize Output Styling?
Adding style to your output isn’t just for looks—it helps you communicate better. Here are main reasons to change output style:
- 🧠 Easier for Readers: Styled outputs help readers find main points fast, without reading through long logs.
- 🎯 Showing What’s Important: Use color, bold text, or size to make important numbers or findings stand out.
- 🏢 Matching Your Look: Using the same fonts and brand colors makes your reports match your team’s or company’s style.
- ♿ Helping People Read: Using bigger text and good color contrast makes reports easier for people with sight problems to read.
- 📊 Adding Notes Based on Data: You can add style based on values (like red text for p-values over 0.05). This helps make reports that react to the data.
Whether you’re making a report for a client or building research files, styling is a key part of communication.
Using HTML/CSS with message() and print()
Simply put, you can use HTML code right in your text to change how text looks:
cat('<span style="color:red; font-size:14px;">', "Important output", '</span>')
This works well for results or summaries you show yourself. But it won’t change output from base R functions that use message() or print(). That’s because:
print()sends output normally.message()is handled like a special message.
These types of output are processed separately by knitr. You need a more advanced method using custom hooks to stop and style them everywhere.
Customizing with knitr Chunk Options
Code chunks in R Markdown have options that control how output acts. A common chunk line might look like this:
```{r results-chunk, message=TRUE, warning=FALSE, results="asis"}
These settings mean:
message=TRUE: show messages from the code.warning=FALSE: hide warnings.results='asis': lets raw results (like HTML) show up as they are.
But remember: chunk options control if output shows, not how it looks. To change font, color, or structure, you need to go one step further—into knitr hooks.
Using knitr Hooks for Advanced Customization
Hooks let you control things well and for many reports when R Markdown processes output.
Here’s how to change the font color and size of all messages in your document everywhere:
knitr::knit_hooks$set(message = function(x, options) {
paste0('<span style="color:blue; font-size:16px;">', x, '</span>')
})
This code should go in a setup chunk, usually the first code chunk in your document:
```{r setup, include=FALSE}
knitr::opts_chunk$set(message = TRUE, warning = TRUE, echo = TRUE)
knitr::knit_hooks$set(
message = function(x, options) {
paste0('<span style="color:blue; font-size:16px;">', x, '</span>')
},
warning = function(x, options) {
paste0('<span style="color:orange;">', x, '</span>')
}
)
Now, whatever you send using message() or warning() will have this style everywhere.
Output hooks are also available and can style printed output from functions:
knitr::knit_hooks$set(output = function(x, options) {
paste0('<div style="color:#444444; font-size:14px;">', x, '</div>')
})
You can change hooks more, for example, to style output based on what it says (like make it red if a warning has “fail”).
Styling print() Output with HTML Wrapping
Unlike message(), print() isn’t usually stopped automatically for styling. But you can catch and style printed output yourself using capture.output():
captured <- capture.output(print(summary(mtcars)))
cat(sprintf('<div style="color:green; font-size:13px;">%s</div>', paste(captured, collapse = "<br>")))
What happens here?
capture.output()gets the printed text and puts it into a list of words.paste(..., collapse = "<br>")changes it to work with HTML line breaks.cat()puts it inside a<div>tag with styles right there.
This method gives you full HTML/CSS styling freedom, even for complex things like tables or stats summaries.
HTML-Specific Considerations and Output Format Compatibility
Remember that HTML styling added right in the text mainly works in HTML papers. Here’s what to know about other types:
- PDF (via LaTeX): HTML tags are ignored. To style output, you have to set up LaTeX commands or use special packages like
kableExtrathat work with LaTeX. - Word: Often ignores the styles and uses Word’s standard ones. Use Word reference files or add styles by hand after saving.
- HTML: Uses the styles fully, making it the best type for changing how things look easily.
When working with different types, set up things to check which type is being made using the rmarkdown::pandoc_to() function and change styles based on that.
Creating Reusable Output Styling Functions
If you use the same cat() and styling many times, make a helper function:
styled_message <- function(msg, color = "green", size = "13px") {
cat(sprintf('<span style="color:%s; font-size:%s;">%s</span>', color, size, msg))
})
Using it is simple:
styled_message("All tests passed")
styled_message("Warning: Model did not converge", color = "red", size = "14px")
This helps with:
- Following the DRY rule (Don’t Repeat Yourself)
- Making sure styles are the same in the whole report
- Making your code chunks easier to read and update
Using Custom Themes and Templates
For styles that are the same across the whole paper:
- External CSS: Put styles in
styles.cssand link it in the YAML header:
output:
html_document:
css: "styles.css"
Example content of styles.css:
span.message {
color: navy;
font-weight: bold;
}
div.output {
font-size: 14px;
color: #444;
margin-bottom: 1em;
}
And then update your hooks to match:
knitr::knit_hooks$set(message = function(x, options) {
paste0('<span class="message">', x, '</span>')
})
- Custom Templates: Make R Markdown templates you can use again. These can set up options, hooks, and even how the page looks. This is very useful for teams working together.
Styling Do’s and Don’ts
✅ Do:
- Use output hooks to add uniform style to
message(),warning(), andprint()output. - Keep font sizes between 12px–16px for readability.
- Maintain adequate color contrast for accessibility compliance (WCAG standards).
🚫 Don’t:
- Overuse styles—limit bold colors to key insights.
- Rely on inline styling for Word/PDF without confirming rendering behavior.
- Ignore mobile responsiveness if embedding in web platforms.
Common Pitfalls and How to Fix Problems
Here are some common issues and how to fix problems:
- HTML Tags Not Showing: Check that your paper is made into HTML, and
results='asis'is set for chunks that need it. - Message Output Still Plain: Make sure you set up the hook right and that it ran in a chunk early in the paper.
- Chunk Options Not Working: Check the chunk line format again—YAML must be written exactly right.
- HTML Code Showing: Clean up content if people can add text (to stop bad HTML code).
- Looks Different in Different Types: Use
rmarkdown::pandoc_to()inside chunks to see what kind of paper is being made and change styles based on that.
Additional Resources
Want to learn more about changing output? Look at:
- Xie, Y. (2015). Dynamic Documents with R and knitr (2nd ed.). CRC Press.
- RStudio. (n.d.). R Markdown: The Definitive Guide. Retrieved from https://bookdown.org/yihui/rmarkdown/
- Broman, K. W. (2014). Knitr and reproducible research. Madison: University of Wisconsin.
These resources give good info on how reports are made, changing hooks, templates, using CSS, how it works with LaTeX, and why reproducible R Markdown work is important.
Whether you are making a report on data or a dashboard for people to make decisions, thinking about how output looks makes your work go from just working to looking professional. Using knitr hooks, functions you can use again for styling, and HTML/CSS, you’ll make things clearer. And you’ll make reports that look better than people might expect.
Citations
Xie, Y. (2015). Dynamic Documents with R and knitr (2nd ed.). CRC Press.
RStudio. (n.d.). R Markdown: The Definitive Guide. Retrieved from https://bookdown.org/yihui/rmarkdown/
Broman, K. W. (2014). Knitr and reproducible research. Madison: University of Wisconsin.
