10 Figures, Tables, Captions.

You need figures and tables in your own writing, whether it be a journal paper, an internal document, or some documentation. In this section, we discuss how to add figures and tables into your R Markdown document, and how to provide captions for them.

10.1 Overview

• Teaching 10 minutes
• Exercises 10 minutes

10.2 Questions

• How do I create a figure in R Markdown?
• How do I create a table in R Markdown?
• How do I add captions for figures and tables?

10.3 Objectives

10.4 Tables

To produce a table, I recommend you use the kable function from the knitr package.

10.4.1 Demo

kable takes a data.frame as input, and outputs the table into a markdown table, which will get rendered into the appropriate output format.

For example, let’s say we wanted to share the first 6 rows of our gapminder data.

This gives us the following output

top_gap <- head(gapminder)

knitr::kable(top_gap)

country	continent	year	lifeExp	pop	gdpPercap
Afghanistan	Asia	1952	28.801	8425333	779.4453
Afghanistan	Asia	1957	30.332	9240934	820.8530
Afghanistan	Asia	1962	31.997	10267083	853.1007
Afghanistan	Asia	1967	34.020	11537966	836.1971
Afghanistan	Asia	1972	36.088	13079460	739.9811
Afghanistan	Asia	1977	38.438	14880372	786.1134

So how does that work? kable prints out the following:

|country     |continent | year| lifeExp|      pop| gdpPercap|
|:-----------|:---------|----:|-------:|--------:|---------:|
|Afghanistan |Asia      | 1952|  28.801|  8425333|  779.4453|
|Afghanistan |Asia      | 1957|  30.332|  9240934|  820.8530|
|Afghanistan |Asia      | 1962|  31.997| 10267083|  853.1007|
|Afghanistan |Asia      | 1967|  34.020| 11537966|  836.1971|
|Afghanistan |Asia      | 1972|  36.088| 13079460|  739.9811|
|Afghanistan |Asia      | 1977|  38.438| 14880372|  786.1134|

And this then gets rendered as a table. This works for HTML, PDF, and Word!

10.4.1.1 Adding captions to a table

Now, say that we wanted to include a caption? We use the caption argument.

knitr::kable(top_gap,
             caption = "The first 6 rows of the dataset, gapminder")

Table 10.1: The first 6 rows of the dataset, gapminder

country	continent	year	lifeExp	pop	gdpPercap
Afghanistan	Asia	1952	28.801	8425333	779.4453
Afghanistan	Asia	1957	30.332	9240934	820.8530
Afghanistan	Asia	1962	31.997	10267083	853.1007
Afghanistan	Asia	1967	34.020	11537966	836.1971
Afghanistan	Asia	1972	36.088	13079460	739.9811
Afghanistan	Asia	1977	38.438	14880372	786.1134

Some other useful features of kable include setting the rounding number, with the digits option.

For example, we could present the first 2 digits of each number like so:

knitr::kable(top_gap,
             caption = "The first 6 rows of the dataset, gapminder",
             digits = 2)

Table 10.2: The first 6 rows of the dataset, gapminder

country	continent	year	lifeExp	pop	gdpPercap
Afghanistan	Asia	1952	28.80	8425333	779.45
Afghanistan	Asia	1957	30.33	9240934	820.85
Afghanistan	Asia	1962	32.00	10267083	853.10
Afghanistan	Asia	1967	34.02	11537966	836.20
Afghanistan	Asia	1972	36.09	13079460	739.98
Afghanistan	Asia	1977	38.44	14880372	786.11

There are other options that you can set in kable, but for these options will get you through a large majority of what you need. For more information on what kable can provide, see ?knitr::kable.

There are many different ways to produce tables in R. We have chosen to show kable today because kable is minimal, but powerful. If you want to extend kable to do more, look at kableExtra, in particular the option kableExtra::kable_styling(latex_options = c("hold_position")).

10.4.2 Your Turn

1. Create a summary of your gapminder data, and put it into a table.
2. Add a caption to this table
3. Set the number of decimals to 2.

10.5 Figures

Printing figures is probably my favourite feature of R Markdown. It is actually relatively straightforward in the case of plots. You provide the plot you want to show in a code chunk!

10.5.0.1 Demo

For example, I can print a plot of the gapminder data for Australia like so:

library(ggplot2)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

gapminder %>%
  filter(country == "Australia") %>%
  ggplot(aes(x = year,
             y = lifeExp)) + 
  geom_point()

10.5.1 Captions for figures

Inserting a caption for a figure is a little bit different. The caption argument is controlled in the chunk option, under the option, fig.cap.

So to insert a figure, we do the following.

``{r gg-oz-gapminder, fig.cap = "Life expectancy from 1952 - 2007 for Australia. Life expentancy increases steadily except from 1962 to 1969. We can safely say that our life expectancy is higher than it has ever been!"}
library(ggplot2)
library(dplyr)

gapminder %>%
  filter(country == "Australia") %>%
  ggplot(aes(x = lifeExp,
             y = year)) + 
  geom_point()
```

Which would produce the following output

library(ggplot2)
library(dplyr)

gapminder %>%
  filter(country == "Australia") %>%
  ggplot(aes(x = lifeExp,
             y = year)) + 
  geom_point()

Figure 10.1: Life expectancy from 1952 - 2007 for Australia. Life expentancy increases steadily except from 1962 to 1969. We can safely say that our life expectancy is higher than it has ever been!

10.5.2 Your Turn

• Create a plot with your .Rmd doc
• Add a figure caption

10.5.3 Inserting images

We cannot always generate the graphics that we want - for example, we might have an image of something that we want to show, or perhaps a nice flowchart someone else made.

In our case, say we wanted to insert the APPS logo into our document, there are two ways we can do this.

1. With markdown syntax
2. with knitr::include_graphics()

Markdown syntax

The markdown syntax to insert an image is: ![caption]("path/to/image")

10.5.3.1 Demo

So we could insert the APPS 50 Years logo by doing the following:

```
![APPS 50 Years Logo!](/figs/logo-apps.png)
```

Which would give us the following output:

APPS 50 Years Logo!

But say that we want more control over the output, like we want to center the image, and we want to make it smaller? Then you can use knitr::include_graphics(), and control the figure size using the options out.width, and add a caption with fig.cap.

``{r logo-apps, fig.align = 'center', out.width = "25%", fig.cap = "The APPS logo for our 50th year!"}
knitr::include_graphics(here::here("figs", "logo-apps.png"))
```

knitr::include_graphics(here::here("figs", "logo-apps.png"))

Figure 10.2: The APPS logo for our 50th year!

`

10.5.4 Your Turn

1. Download the gapminder logo and put it into a new directory call “figs”
2. Insert this image into your R Markdown document around where you introduce gapminder.

10.6 Summary

We’ve now learned how to insert tables, plots, and images into our documents!