088-r_marky_markdown-patchwork.Rmd

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)

library(tidyverse)
library(flair)
library(here)
```

# Multiple plots with `patchwork`

*Written by Michael Chong and last updated on 7 October 2021.*

## Introduction

In this lesson, you will learn how to:

- use the [`patchwork`](https://patchwork.data-imaginist.com/) R package to make multi-panel plots

Prerequisite skills include:

- familiarity with `ggplot()`


## What is `patchwork`?

In some situations it might be useful to arrange multiple plots side by side. The `patchwork` R package provides a really easy way to do this.

[The package website](https://patchwork.data-imaginist.com/) is a great resource on its own. Most of the content in this lesson can also be found there.

**To get started**, make sure to have the package installed, which you can get using the default install command:

```{r, eval = FALSE}
install.packages("patchwork")
```

and load the package:

```{r}
library(patchwork)
```


## Getting started

First, make some plots that you want to put together. Here's an example using the [`palmerpenguins`](https://allisonhorst.github.io/palmerpenguins/index.html) dataset. 

```{r}
library(palmerpenguins)

# Make a scatterplot of flipper length vs. body mass
first_plot <- ggplot(penguins, aes(x = flipper_length_mm, y = body_mass_g)) +
  geom_point()

# Make a boxplot of body mass by sex
second_plot <- ggplot(penguins, aes(x = sex, y = body_mass_g)) +
  geom_boxplot()
```

Putting two plots together is as simple as just "adding" them with a `+` sign:

```{r, warning = FALSE}
# Add them together side by side
first_plot + second_plot
```

If we want to stack the plots on top of each other, we use the `/` symbol instead:

```{r, warning = FALSE}
# Stack them on top
first_plot / second_plot
```

It's that simple!

## More complicated layouts

Okay, what if you have more than 2 plots that you want to arrange? Suppose we also want to plot how size varies by island.

```{r, warning = FALSE}
third_plot <- ggplot(penguins, aes(x = island, y = body_mass_g)) +
  geom_boxplot()
```

To put them in a row, I'd recommend using `|` (instead of `+`, which doesn't always force them in a row)

```{r, warning = FALSE}
first_plot | second_plot | third_plot
```

or, you can stack as many as you want by adding more `/` symbols:

```{r, warning = FALSE}
first_plot / second_plot / third_plot
```

Or, you can arrange them using a mix of `|` and `/`:

```{r, warning = FALSE}
first_plot | second_plot / third_plot
```

You can use parentheses `( )` to change "the order of operations" to change how things are arranged:

```{r, warning = FALSE}
(first_plot | second_plot) / third_plot
```

With these few tools, you can get good looking multi-panel plots relatively easily!

## Customization and annotation

After you have the plots arranged in the way you want, maybe you want to add a title and labels, which you can do using the `plot_annotation()` function. You can just add this to the `patchwork` expression.

As an example, I'll add a title, subtitle, caption, as well as "tag" the individual subplots with "a", "b", "c".

```{r, warning = FALSE}
(first_plot | second_plot / third_plot) +
  plot_annotation(
    title = "Exploration of penguin size",
    subtitle = "I love penguins!",
    caption = "Here goes a descriptive caption explaining the plots.",
    tag_levels = "a"
  )
```

Note that I have to wrap `first_plot | second_plot / third_plot` in parentheses `( )` -- otherwise the annotations won't be added correctly. You can also assign the patchwork as its own object before adding the annotations:

```{r, warning = FALSE}
my_patchwork <- first_plot | second_plot / third_plot
```


The arguments for `title`, `subtitle`, and `caption` are straightforward -- you just provide a string of text to display.

For `tag_levels`, you specify how you want the subplots to be labelled. You can provide:

* `a` for lowercase letters (shown above),
* `A` for uppercase letters,
* `1` for numbers,
* `i` or `I` for lowercase or uppercase Roman numerals

Remember you can always check how to use the function using `?plot_annotation`.


## Exercises

### Exercise 1

```{r, echo = FALSE, warning = FALSE}
(first_plot / first_plot) | first_plot 
```

Using the plot `first_plot` three times, recreate the `patchwork` layout above.

```{r patchwork-exercise-1, exercise = TRUE, warning = FALSE}

```

```{r patchwork-exercise-1-solution, warning = FALSE}
(first_plot / first_plot) | first_plot
```

### Exercise 2 

Annotate the plot you made in Exercise 1! Replicate the following:

```{r, echo = FALSE, warning = FALSE}
first_plot_modified <- first_plot + labs(title = "This plot has its own title")

((first_plot / first_plot) | first_plot_modified) +
  plot_annotation(
    title = "The same plot...three times!",
    caption = "What a great caption!"
  )
```

```{r patchwork-exercise-2, exercise = TRUE, warning = FALSE}

```

```{r patchwork-exercise-2-hint-1, warning = FALSE, eval = FALSE}
You'll need to modify one of the subplots.
```

```{r patchwork-exercise-2-solution, warning = FALSE}
first_plot_modified <- first_plot + labs(title = "This plot has its own title")

((first_plot / first_plot) | first_plot_modified) +
  plot_annotation(
    title = "The same plot...three times!",
    caption = "What a great caption!"
  )
```

## Common Mistakes & Errors

**Annotations aren't showing up** You might need to make sure you're adding the `plot_annotation()` to the patchwork object. Try wrapping your patchwork in parentheses (e.g. `(plot1 | plot2) + plot_annotation(...)`), or saving it to a different object first (`patchwork <- plot1 | plot2; patchwork + plot_annotation(...)`)

**I'm having trouble laying out my plots how I want** Check out some of the resources under Next Steps -- in particular browsing the patchwork website. This lesson just introduces some of the basic functionality, and there's lots more to know!

**`Error: Can't add ____ to a ggplot object`** First, make sure you've loaded the `patchwork` package with `library(patchwork)`. Then, make sure that all the plots you're trying to add together are `ggplot` objects (see code chunk below). 

```{r, warning = FALSE}
class(first_plot)
```

**patchwork and `plot()`** Note that plots made using base R's `plot()` function aren't compatible with patchwork (as far as I know)! If you need to put base R plots together in a similar way, you can try using the `cowplot` R package. 

## Next Steps

If you need more functionality, the `patchwork` package is capable of much more! You can browse the [main website](https://patchwork.data-imaginist.com/index.html) or check out these vignettes:

* [More advanced layouts](https://patchwork.data-imaginist.com/articles/guides/layout.html)
* [Alignment across multiple pages](https://patchwork.data-imaginist.com/articles/guides/multipage.html)

If you still need more functionality to get those plots perfectly arranged, you can try the [`cowplot` package](https://wilkelab.org/cowplot/index.html). It's more powerful, but the syntax is a bit more difficult.



## Exercises

### Question 1

### Question 2

### Question 3

### Question 4

### Question 5

### Question 6

### Question 7

### Question 8

### Question 9

### Question 10