rmd4sci

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 rmarkdown document, and how to provide captions for them.

Overview

Teaching 10 minutes
Exercises 10 minutes

Questions

How do I create a figure in rmarkdown?
How do I create a table in rmarkdown?
How do I add captions for figures and tables?

Objectives

Tables

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

Demo {.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!

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: (#tab:print-tab-gap-captions)The first 6 rows of the dataset, gapminder

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: (#tab:print-tab-gap-digits)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")).

Your Turn {.exercise}

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

Figures

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

Demo {.demo}

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

library(ggplot2)

## Registered S3 methods overwritten by 'ggplot2':
##   method         from 
##   [.quosures     rlang
##   c.quosures     rlang
##   print.quosures rlang

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()

Captions for figures {.demo}

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()

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!

(\#fig:gg-oz-gapminder)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!

Your Turn {.exercise}

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

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 new SSA logo into our document, there are two ways we can do this.

With markdown syntax
with knitr::include_graphics()

Markdown syntax

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

Demo {.demo}

So we could insert the new SSA vic logo by doing the following:

```
![SSA Logo!](bit.ly/ssa-vic)
```

Which would give us the following output:

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 ssa-logo, fig.align = 'center', out.width = "25%", fig.cap = "The new SSA logo, which is actually a scatterplot, which is super neat!"}
knitr::include_graphics(here::here("figs", "ssa-logo.png"))
```

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

(\#fig:ssa-logo)The new SSA logo, which is actually a scatterplot, which is super neat!

Your Turn {.exercise}

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

Summary

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

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