Pimp my RMD: a few tips for R Markdown
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R markdown creates interactive reports from R code. This post provides a few tips I use on a daily basis to improve the appearance of output documents. In any case, an unavoidable resource is the Rstudio documentation.

Text formating

R markdown allows to easily format your text. You can add links, write in bold or italic. This is very well explained in the Rstudio cheatsheet.

Here is the code I used to make this paragraph:

R markdown allows to easily format your text. You can add [links](www.r-graph-gallery.com), write in **bold** or *italic*. This is very well explained in the [Rstudio cheatsheet](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf).

Horizontal lines

Add an horizontal line by adding 3 stars:

***

Chapter auto numbering

Header of level 1, 2, 3 are set using #, ## and ###. You can auto number your chapters using this option in the header:

---
title: "Your title"
output: 
  html_document:
    number_sections: TRUE
---

# Title
## A subtitle
## Another subtitle

# Another title

Skip a line

I really like to add spaces in my document to give it a more uncluttered look. This is done using the <br> command. This .rmd code:

A first sentence
<br><br><br><br>
A seconde sentence

will give this htmloutput:

A first sentence



A seconde sentence

Center an image

To center an image, use this code:

<center>
![FigName](logo_r_graph_gallery.jpg)
</center>
Here is the result
FigName

White space around img

If you’re struggling with to much white space around your image, try to play with the fig.asp argument. Here I used fig.asp=0.50.

library(png)
library(grid)
img <- readPNG("kan.png")
grid.raster(img)
Lovely Kangaroo from the Mornington Peninsula.

Lovely Kangaroo from the Mornington Peninsula.

Note: thanks to Anna Quaglieri for this suggestion.

Space before title

I find it pleasant to have a bit of space before starting a new chapter. You can use a <br> before each header. A more convenient way is to add some margin in your CSS. Create a style.css file:

h1, .h1, h2, .h2, h3, .h3 {
    margin-top: 84px;
}

A rmd document that takes into account this .css file:

---
title: "A document with a CSS included"
output:
  html_document:
    css: style.css
---

A title will follow, but with a lot of space before it

# Title 1

content of part 1

# Title 2

content of part 2

The document you are reading uses this css. See the separation between chapters.

Figures caption

Specify the caption of your figure in the chunk header. Example:

{r, fig.align="center", fig.width=6, fig.height=6, fig.cap="Figure: Here is a really important caption."}
library(tidyverse)
mpg %>%
  ggplot( aes(x=reorder(class, hwy), y=hwy, fill=class)) + 
    geom_boxplot() +
    xlab("class") +
    theme(legend.position="none")
Figure: Here is a really important caption.

Figure: Here is a really important caption.

Custom caption

Change the black default caption using CSS. Adding this code in your style.css file.

<style>
p.caption {
  font-size: 0.9em;
  font-style: italic;
  color: grey;
  margin-right: 10%;
  margin-left: 10%;  
  text-align: justify;
}
</style>
file will give this result: