r4ds/visualize.Rmd

# Data visualisation

> "The simple graph has brought more information to the data analyst’s mind 
> than any other device." --- John Tukey

This chapter will teach you how to visualize your data with R and ggplot2. R contains several systems for making graphs, but the ggplot2 system is one of the most beautiful and most versatile. ggplot2 implements the __grammar of graphics__, a coherent system for describing and building graphs. With ggplot2, you can do more faster by learning one system and applying it in many places.

## Prerequisites

To access the datasets, help pages, and functions that we will use in this chapter, load ggplot2 using the `library()` function. We'll also load tibble, which you'll learn about later. It improves the default printing of datasets.

```{r setup}
library(ggplot2)
library(tibble)
```

If you run this code and get the error there is no package called ‘ggplot2’, you'll need to first install it, and then run `library()` once again.

```{r eval = FALSE}
install.packages("ggplot2")
library(ggplot2)
```

You only need to install a package once, but you need to reload it every time you start a new session.

If we need to be explicit about where a function (or dataset) comes from, we'll use the special form `package::function()`. For example, `ggplot2::ggplot()` tells you explicitly that we're using the `ggplot()` function from the ggplot2 package.

## A graphing template

Let's use our first graph to answer a question: Do cars with big engines use more fuel than cars with small engines? You probably already have an answer, but try to make your answer precise. What does the relationship between engine size and fuel efficiency look like? Is it positive? Negative? Linear? Nonlinear?

You can test your answer with the `mpg` dataset in ggplot2, or `ggplot2::mpg`:

```{r}
mpg
```

The dataset contains observations collected by the EPA on 38 models of car. Among the variables in `mpg` are:

1. `displ` - a car's engine size in litres, and 

1. `hwy` - a car's fuel efficiency on the highway in miles per gallon (mpg). 
  A car with a low fuel efficiency consumes more fuel than a car with a high 
  fuel efficiency when they travel the same distance. 

To learn more about `mpg`, open its help page with the command `?mpg`.

To plot `mpg`, open an R session and run the code below. The code plots the `mpg` data by putting `displ` on the x-axis and `hwy` on the y-axis:

```{r}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy))
```

The plot shows a negative relationship between engine size (`displ`) and fuel efficiency (`hwy`). In other words, cars with big engines use more fuel. Does this confirm or refute your hypothesis about fuel efficiency and engine size?

Pay close attention to this code because it is almost a template for making plots with ggplot2.

```{r eval=FALSE}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy))
```

With ggplot2, you begin a plot with the function `ggplot()`. `ggplot()` creates a coordinate system that you can add layers to. The first argument of `ggplot()` is the dataset to use in the graph. So `ggplot(data = mpg)` creates an empty graph that will use the `mpg` dataset:

```{r}
ggplot(data = mpg)
```

You complete your graph by adding one or more layers to `ggplot()`. Here, the function `geom_point()` adds a layer of points to your plot, which creates a scatterplot. ggplot2 comes with many geom functions that each add a different type of layer to a plot. 

Each geom function in ggplot2 takes a mapping argument. The mapping argument of your geom function explains where your points should go. You must set `mapping` to a call to `aes()`. The `x` and `y` arguments of `aes()` explain which variables to map to the x and y axes of your plot. `ggplot()` will look for those variables in your dataset, `mpg`.

Let's turn this code into a reusable template for making graphs with ggplot2. To make a graph, replace the bracketed sections in the code below with a dataset, a geom function, or a set of mappings.

```{r eval = FALSE}
ggplot(data = <DATA>) + 
  <GEOM_FUNCTION>(mapping = aes(<MAPPINGS>))
```

The rest of this chapter will show you how to complete and extend this template to make different types of graphs. We will begin with the `<MAPPINGS>` component.

## Aesthetic mappings

> "The greatest value of a picture is when it forces us to notice what we
> never expected to see." --- John Tukey

In the plot below, one group of points seems to fall outside of the linear trend. These cars have a higher mileage than you might expect. How can you explain these cars? 

```{r, echo = FALSE}
knitr::include_graphics("images/visualization-1.png")
```

Let's hypothesize that the cars are hybrids. One way to test this hypothesis is to look at the `class` value for each car. The `class` variable of the `mpg` dataset classifies cars into groups such as compact, midsize, and suv. If the outlying points are hybrids, they should be classified as compact cars or, perhaps, subcompact cars (keep in mind that this data was collected before hybrid trucks and suvs became popular).

You can add a third variable, like `class`, to a two dimensional scatterplot by mapping it to an _aesthetic_.

An aesthetic is a visual property of the objects in your plot. Aesthetics include things like the size, the shape, or the color of your points. You can display a point (like the one below) in different ways by changing the values of its aesthetic properties. Since we already use the word "value" to describe data, let's use the word "level" to describe aesthetic properties. Here we change the levels of a point's size, shape, and color to make the point small, triangular, or blue.

```{r, echo = FALSE}
knitr::include_graphics("images/visualization-2.png")
```

You can convey information about your data by mapping the aesthetics in your plot to the variables in your dataset. For example, you can map the colors of your points to the `class` variable to reveal the class of each car.

```{r}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy, color = class))
```

(If you prefer British English, like Hadley, you can use `colour` instead of `color`.)

To map an aesthetic to a variable, set the name of the aesthetic to the name of the variable, _and do this in your plot's `aes()` call_. ggplot2 will automatically assign a unique level of the aesthetic (here a unique color) to each unique value of the variable, a process known as _mapping_. ggplot2 will also add a legend that explains which levels correspond to which values.

The colors reveal that many of the unusual points are two seater cars. These cars don't seem like hybrids. In fact, they seem like sports cars---and that's what they are. Sports cars have large engines like suvs and pickup trucks, but small bodies like midsize and compact cars, which improves their gas mileage. In hindsight, these cars were unlikely to be hybrids since they have large engines.

In the above example, we mapped `class` to the color aesthetic, but we could have mapped `class` to the size aesthetic in the same way. In this case, the exact size of each point would reveal its class affiliation. 

```{r}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy, size = class))
```

Or we could have mapped `class` to the _alpha_ aesthetic, which controls the transparency of the points. Now the transparency of each point corresponds to its class affiliation. 

```{r}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy, alpha = class))
```

We also could have mapped `class` to the shape of the points.

```{r warning=FALSE}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy, shape = class))
```

What happened to the suvs? ggplot2 will only use six shapes at a time. Additional groups will go unplotted when you use this aesthetic.

For each aesthetic, you set the name of the aesthetic to the variable to display, and you do this within the `aes()` function. The `aes()` function gathers together each of the aesthetic mappings used by a layer and passes them to the layer's mapping argument. The syntax highlights a useful insight about `x` and `y`: the x and y locations of a point are themselves aesthetics, visual properties that you can map to variables to display information about the data. 

Once you set an aesthetic, ggplot2 takes care of the rest. It selects a pleasing set of levels to use for the aesthetic, and it constructs a legend that explains the mapping between levels and values. For x and y aesthetics, ggplot2 does not create a legend, but it creates an axis line with tick marks and a label. The axis line acts as a legend; it explains the mapping between locations and values.

You can also set the aesthetic properties of your geom manually. For example, we can make all of the points in our plot blue. 

```{r}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy), color = "blue")
```

Here, the color doesn't convey information about a variable. It only changes the appearance of the plot. To set an aesthetic manually, do not place it in the `aes()` function. Call the aesthetic by name as an argument of your geom function. Then pass the aesthetic a level that R will recognize, such as 

* the name of a color as a character string.
* the size of a point in mm.
* the shape as a point as a number, as shown below.

R uses the following numeric codes to refer to the following shapes. 

```{r echo = FALSE}
shapes <- tibble(
  shape = c(0:19, 22, 21, 24, 23, 20),
  x = 0:24 %/% 5,
  y = -(0:24 %% 5)
)
ggplot(shapes, aes(x, y)) + 
  geom_point(aes(shape = shape), size = 5, fill = "red") +
  geom_text(aes(label = shape), hjust = 0, nudge_x = 0.15) +
  scale_shape_identity() +
  expand_limits(x = 4.1) +
  scale_x_continuous(NULL, breaks = NULL) + 
  scale_y_continuous(NULL, breaks = NULL)
```

If you get an odd result, double check that you are calling the aesthetic as its own argument (and not calling it from inside of `mapping = aes()`). I like to think of aesthetics like this, if you place the aesthetic: 

* _inside_ of the `aes()` function, ggplot2 will **map** the aesthetic to data 
  values and build a legend.

* _outside_ of the `aes()` function, ggplot2 will **set** the aesthetic to a 
  level that you supply manually.

### Exercises

1.  Which variables in the `mpg` are discrete? Which variables are continuous? 
    (Hint: type `?mpg` to read the documentation for the dataset). How 

1.  Map a discrete variable to `color`, `size`, and `shape`. Then map a
    continuous variable to each aesthetic. How does ggplot2 behave differently for 
    discrete vs. continuous variables? 
    
1.  What happens if you map multiple variables to the same aesthetic? 
    What happens when you map multiple variables to different aesthetics?
  
1.  What other aesthetics can `geom_point()` take? (Hint: use `?geom_point`)
    
1.  What happens if you set an aesthetic to something other than a variable 
    name, like `displ < 5`?

1.  What happens if you accidentally write this code? Why are the points
    not blue?

    ```{r}
    ggplot(data = mpg) + 
      geom_point(mapping = aes(x = displ, y = hwy, color = "blue"))
    ```
    
1.  Vignettes are long-form guides the documentation things about 
    a package that affect many functions. ggplot2 has two vignettes
    what do they describe?

## Facets

One way to add additional variables is with aesthetics. Another way, particularly useful for categorical variables is to split your plot into _facets_, subplots that each display a subset of the data. 

To facet your plot, add `facet_wrap()` to your plot call. The first argument of `facet_wrap()` is a formula, which you create with `~` followed by a variable name (here "formula" is the name of a data structure in R, not a synonym for "equation"). The variable that you pass to `facet_wrap()` should be discrete. 

Here we create a separate subplot for each level of the `clarity` variable. The first subplot displays the group of points that have the `clarity` value `I1`. The second subplot displays the group of points that have the `clarity` value `SI2`. And so on.

```{r fig.width = 7, out.width = "100%"}
ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) + 
  geom_point() + 
  facet_wrap(~ class, nrow = 2)
```

To facet your plot on the combination of two variables, add `facet_grid()` to your plot call. The first argument of `facet_grid()` is also a formula. This time the formula should contain two variable names separated by a `~`. 

```{r fig.height = 7, out.width = "100%"}
ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) + 
  geom_point() + 
  facet_grid(drv ~ cyl)
```

If you prefer to not facet on the rows or columns dimension, place a `.` instead of a variable name before or after the `~`, e.g. `+ facet_grid(. ~ clarity)`.

### Exercises

1.  What plots will the following code make? What does `.` do?

    ```{r eval = FALSE}
    ggplot(data = mpg) + 
      geom_point(mapping = aes(x = displ, y = hwy)) +
      facet_grid(drv ~ .)
    
    ggplot(data = mpg) + 
      geom_point(mapping = aes(x = displ, y = hwy)) +
      facet_grid(. ~ cyl)
    ```

1.  Take the first faceted plot in this section:

    ```{r}
    ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) + 
      geom_point() + 
      facet_wrap(~ class, nrow = 2)
    ```
    
    What are the advantages to using facetting instead of the colour aesthetic?
    What are the disadvantages? How might the balance of the two change if you
    had a larger dataset?
    
1.  Read `?facet_wrap`. What does `nrows` do? What does `ncols` do? What other
    options control the layout of the individual panels?

1.  When using `facet_grid()` you should usually put the variable with more
    unique levels in the columns. Why?
    
1.  How might `cut_number()` and `cut_width()` help if you wanted to facet
    by a continuous variable?

## Geometric objects

How are these two plots similar? 

```{r echo = FALSE, out.width = "50%", fig.align="default"}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy))

ggplot(data = mpg) + 
  geom_smooth(mapping = aes(x = displ, y = hwy))
```

Both plots contain the same x variable, the same y variable, and both describe the same data. But the plots are not identical. Each plot uses a different visual object to represent the data. In ggplot2 syntax, we say that they use different _geoms_.

A _geom_ is the geometrical object that a plot uses to represent data. People often describe plots by the type of geom that the plot uses. For example, bar charts use bar geoms, line charts use line geoms, boxplots use boxplot geoms, and so on. Scatterplots break the trend; they use the point geom. As we see above, you can use different geoms to plot the same data. The plot on the left uses the point geom, and the plot on the right uses the smooth geom, a smooth line fitted to the data. 

To change the geom in your plot, change the geom function that you add to `ggplot()`. For instance, to make the plot on the left, use `geom_point()`: 

```{r eval = FALSE}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy))
```

To make the plot on the right use `geom_smooth()`:

```{r eval=FALSE, message = FALSE}
ggplot(data = mpg) + 
  geom_smooth(mapping = aes(x = displ, y = hwy))
```

Every geom function in ggplot2 takes a `mapping` argument. However, not every aesthetic works with every geom. You could set the shape of a point, but you couldn't set the "shape" of a line. On the other hand, you _could_ set the linetype of a line. `geom_smooth()` will draw a different line, with a different linetype, for each unique value of the variable that you map to linetype.

```{r message = FALSE}
ggplot(data = mpg) + 
  geom_smooth(mapping = aes(x = displ, y = hwy, linetype = drv))
```

Here `geom_smooth()` separates the cars into three lines based on their `drv` value, which describes a car's drive train. One line describes all of the points with a `4` value, one line describes all of the points with an `f` value, and one line describes all of the points with an `r` value. Here, `4` stands for four wheel drive, `f` for front wheel drive, and `r` for rear wheel drive.

If this sounds strange, we can make it more clear by overlaying the lines on top of the raw data and then coloring everything according to `drv`. 

```{r echo = FALSE}
ggplot(data = mpg, mapping = aes(x = displ, y = hwy, color = drv)) + 
  geom_point() +
  geom_smooth(mapping = aes(linetype = drv))
```

Notice that this plot contains two geoms in the same graph! If this makes you excited, buckle up. In the next section, we will learn how to place multiple geoms in the same plot.

ggplot2 provides over 30 geom functions that you can use to visualize your data, and extension packages provide even more. Each geom is particularly well suited for visualizing a certain type of data or a certain type of relationship. The table below lists the geoms in ggplot2, loosely organized by the type of relationship that they describe. 

Next to each geom is a visual representation of the geom. Beneath the geom is a list of aesthetics that apply to the geom. Required aesthetics are listed in bold. Many geoms have very useful arguments that help them do their job. For these geoms, we've listed those arguments in the example code.

To learn more about any single geom, open it's help page in R by running the command `?` followed by the name of the geom function, e.g. `?geom_smooth`.

```{r, echo = FALSE, out.width = "100%"}
knitr::include_graphics("images/visualization-geoms-1.png")
knitr::include_graphics("images/visualization-geoms-2.png")
knitr::include_graphics("images/visualization-geoms-3.png")
knitr::include_graphics("images/visualization-geoms-4.png")
```

Many geoms use a single object to describe all of the data. For example, `geom_smooth()` uses a single line. For these geoms, you can set the group aesthetic to a discrete variable to draw multiple objects. ggplot2 will draw a separate object for each unique value of the grouping variable.

In practice, ggplot2 will automatically group the data for these geoms whenever you map an aesthetic to a discrete variable (as in the `linetype` example). It is convenient to rely on this feature because the group aesthetic by itself does not add a legend or distinguishing features to the geoms.

```{r, fig.asp = 1, fig.width = 2.5, fig.align = 'default', out.width = "33%"}
ggplot(diamonds) +
  geom_smooth(aes(x = carat, y = price))
              
ggplot(diamonds) +
  geom_smooth(aes(x = carat, y = price, group = cut))
    
ggplot(diamonds) +
  geom_smooth(aes(x = carat, y = price, color = cut), show.legend = FALSE)
```


To display multiple geoms in the same plot, add multiple geom functions to `ggplot()`! ggplot2 will add each geom as a new layer on top of the previous geoms.

```{r}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy)) +
  geom_smooth(mapping = aes(x = displ, y = hwy))
```

To avoid redundancy, pay attention to your code when you use multiple geoms. Our code now calls `mapping = aes(x = displ, y = hwy)` twice. You can avoid this type of repetition by passing a set of mappings to `ggplot()`. ggplot2 will treat these mappings as global mappings that apply to each geom in the graph. 

```{r}
ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) + 
  geom_point() + 
  geom_smooth()
```

If you place mappings in a geom function, ggplot2 will treat them as local mappings for the layer. It will use these mappings to extend or overwrite the global mappings _for that layer only_. This makes it possible to display different aesthetics in different layers.

```{r}
ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) + 
  geom_point(mapping = aes(color = class)) + 
  geom_smooth()
```

You can use the same idea to specify different `data` for each layer. Here, our smooth line displays just a subset of the `mpg` dataset, the subcompact cars. The local data argument in `geom_smooth()` overrides the global data argument in `ggplot()` for the smooth layer only.

```{r}
ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) + 
  geom_point(mapping = aes(color = class)) + 
  geom_smooth(data = dplyr::filter(mpg, class == "subcompact"), se = FALSE)
```

(Remember, `dplyr::filter()` means call the `filter()` function from dplyr. You'll learn how it works in the next chapter.)

### Exericses

1.  What does `show.legend = FALSE` do?  What happens if you remove it?  
    Why do you think we used it in the example above.

1.  What does the `se` argument to `geom_smooth()` do? (Hint: look at
    `?geom_smooth()`)

1.  What sort of graphic does `geom_boxplot()` produce?

1.  What geom would you use to generate a line plot?

1.  Why might you want to use `geom_count()` when plotting `cty` vs
    `hwy`?

1.  Run this code in your head and predict what the output will look like.
    Run the code in R and check your predictions.
    
    ```{r, eval = FALSE}
    ggplot(data = mpg, mapping = aes(x = displ, y = hwy, color = drv)) + 
      geom_point() + 
      geom_smooth(se = FALSE)
    ```

1.  Will these two graphs look different? Why/why not?

    ```{r, eval = FALSE}
    ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) + 
      geom_point() + 
      geom_smooth()
    
    ggplot() + 
      geom_point(data = mpg, mapping = aes(x = displ, y = hwy)) + 
      geom_smooth(data = mpg, mapping = aes(x = displ, y = hwy))
    ```

1.  Recreate the R code necessary to generate the following graphs.
    
    ```{r, echo = FALSE, fig.width = 4, out.width = "50%", fig.align = "default"}
    ggplot(data = mpg, mapping = aes(x = displ, y = hwy, color = drv)) + 
      geom_point() + 
      geom_smooth(se = FALSE)
    ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) + 
      geom_point(aes(color = drv)) + 
      geom_smooth(se = FALSE)
    ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) + 
      geom_point(aes(group = drv)) + 
      geom_smooth(se = FALSE)
    ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) + 
      geom_smooth(aes(linetype = drv), se = FALSE) + 
      geom_point(aes(color = drv)) 
    ggplot(data = mpg, mapping = aes(x = displ, y = hwy)) + 
      geom_point(size = 4, colour = "white") + 
      geom_point(aes(colour = drv))
    ```

## Statical transformations

Bar charts are interesting because they reveal something subtle about plots. Consider a basic bar chart, as drawn with `geom_bar()`. This chart displays the total number of diamonds in the `diamonds` dataset, grouped by `cut`. The `diamonds` dataset comes in ggplot2 and contains information about ~54,000 diamonds, including the `price`, `carat`, `color`, `clarity`, and `cut` of each diamond. The chart shows that more diamonds are available with high quality cuts than with low quality cuts. 

```{r}
ggplot(data = diamonds) + 
  geom_bar(mapping = aes(x = cut))
```

On the x axis, the chart displays `cut`, a variable in `diamonds`. On the y axis, it displays count; but count is not a variable in `diamonds`! Where does count come from?

Some graphs, like scatterplots, plot the raw values of your dataset. Other graphs, like bar charts, calculate new values to plot:

* **bar charts** and **histograms** bin your data and then plot bin counts, 
  the number of points that fall in each bin.

* **smooth lines** fit a model to your data and then plot the model line.

* **boxplots** calculate the quartiles of your data and then plot the 
  quartiles as a box.

* and so on.

ggplot2 calls the algorithm that a graph uses to calculate new values a __stat__, which is short for statistical transformation. Each geom in ggplot2 is associated with a default stat that it uses to calculate values to plot. The figure below describes how this process works with `geom_bar()`.

```{r, echo = FALSE, out.width = "100%"}
knitr::include_graphics("images/visualization-stat-bar.png")
```

A few geoms, like `geom_point()`, plot your raw data as it is. These geoms also apply a transformation to your data, the identity transformation, which returns the data in its original state. Now we can say that _every_ geom uses a stat.

```{r, echo = FALSE, out.width = "100%"}
knitr::include_graphics("images/visualization-stat-point.png")
```

You can learn which stat a geom uses, as well as what variables it computes by visiting the geom's help page. For example, the help page of `geom_bar()` shows that it uses the count stat and that the count stat computes two new variables, `count` and `prop`. If you have an R session open you can verify this by running `?geom_bar` at the command line.

Stats are the most subtle part of plotting because you do not see them in action. ggplot2 applies the transformation and stores the results behind the scenes. You only see the finished plot. Moreover, ggplot2 applies stats automatically, with a very intuitive set of defaults. As a result, you rarely need to adjust a geom's stat. However, you can do three things with a geom's stat if you wish to.

First, you can change the stat that the geom uses with the geom's stat argument. In the code below, I change the stat of `geom_bar()` from count (the default) to identity. This lets me map to the height of the bars to the raw values of a $y$ variable. 

```{r}
demo <- tibble::tibble(
  a = c("bar_1","bar_2","bar_3"),
  b = c(20, 30, 40)
)
demo

ggplot(data = demo) +
  geom_bar(mapping = aes(x = a, y = b), stat = "identity")
```

(Unfortunately when people talk about bar charts casually, they might be referring to this type of bar chart, where the height of the bar is already present in the data, or the previous bar chart where the height of the bar is generated by counting rows.)

Second, you can give some stats arguments by passing the arguments to your geom function. We saw one earlier when we passed `se = FALSE` to `geom_smooth()`, telling it not to calculate and display the standard errors. In the code below, I pass a width argument to the count stat, which controls the widths of the bars. `width = 1` will make the bars wide enough to touch each other.

```{r}
ggplot(data = diamonds) +
  geom_bar(mapping = aes(x = cut), width = 1)
```

You can learn which arguments a stat takes at the stat's help page. To open the help page, place the prefix `?stat_` before the name of the stat, then run the command at the command line, e.g. `?stat_count`. Often the geom and stat will have the same documentation page so you don't need to jump around.

Finally, you can use extra variables created by the stat. Many stats in ggplot2 create multiple variables, some of which go unused. For example, `geom_count()` uses the "sum" stat to create bubble charts. Each bubble represents a group of data points, and the size of the bubble displays how many points are in the group (e.g. the count of the group).

```{r}
ggplot(data = diamonds) + 
  geom_count(mapping = aes(x = cut, y = clarity))
```

The help page of `?stat_sum` reveals that the sum stat creates two variables, n (count) and prop. By default, `geom_count()` uses the n variable to create the size of each bubble. To tell `geom_count()` to use the prop variable, map $size$ to `..prop..`. The two dots that surround prop notify ggplot2 that the prop variable appears in the transformed dataset that is created by the stat, and not in the raw dataset. Be sure to include these dots whenever you refer to a variable that is created by a stat. 

```{r}
ggplot(data = diamonds) + 
  geom_count(mapping = aes(x = cut, y = clarity, size = ..prop.., group = clarity))
```

For `geom_count()`, the `..prop..` variable does not do anything useful until you set a group aesthetic. If you set _group_ to the $x$ variable, `..prop..` will show proportions across columns. If you set it to the $y$ variable, `..prop..` will show proportions across rows, as in the plot above. Here, the proportions in each row sum to one. 

ggplot2 provides over 20 stats for you to use. Each stat is saved as a function, which provides a convenient way to access a stat's help page, e.g. `?stat_identity`.  The table below describes each stat in ggplot2 and lists the parameters that the stat takes, as well as the variables that the stat makes. 

```{r, echo = FALSE, out.width = "100%"}
knitr::include_graphics("images/visualization-stats.png")
```

### Exercises


## Position adjustments

If you want to color the inside of bars, you need to use the `fill` aesthetic rather than `colour`:

```{r fig.width = 4, out.width = "50%", fig.align = "default"}
ggplot(data = diamonds) + 
  geom_bar(mapping = aes(x = cut, colour = cut))
ggplot(data = diamonds) + 
  geom_bar(mapping = aes(x = cut, fill = cut))
```

If you map the fill aesthetic to another variable, like `clarity`, you get a stacked bar chart. Each colored rectangle represents a combination of `cut` and `clarity`.

```{r}
ggplot(data = diamonds) + 
  geom_bar(mapping = aes(x = cut, fill = clarity))
```

But what if you don't want a stacked bar chart? You can control how ggplot2 deals with overlapping bars using a __position adjustment__ specified by the `position` argument. There are four important options for bars:`"identity"`, `"stack"`, `"dodge"` and `"fill"`.

*   `position = "identity"` will place each object exactly where it falls in 
    the context of the graph. This is not very useful for bars, because it
    overlaps them. To see that overlapping we either need to make the bars
    slightly transparent by setting `alpha`, or completely transparent.
    
    ```{r, fig.width = 4, out.width = "50%", fig.align = "default"}
    ggplot(data = diamonds, mapping = aes(x = cut, fill = clarity)) + 
      geom_bar(alpha = 1/5, position = "identity")
    ggplot(data = diamonds, mapping = aes(x = cut, colour = clarity)) + 
      geom_bar(fill = NA, position = "identity")
    ```
    
    The identity position adjustment is more useful for 2d geoms, where it
    is the default.

*   `position = "stack"` is the default position adjustment for bars, as
    you've seen above.
    
*   `position = "fill"` work like stacking, but makes each set of stacked bars
    the same height. This makes it easier to compare proportions across 
    groups.

    ```{r}
    ggplot(data = diamonds) + 
      geom_bar(mapping = aes(x = cut, fill = clarity), position = "fill") +
      ggtitle('Position = "fill"')
    ```

*   `position = "dodge"` places overlapping objects directly _beside_ one 
    another. This makes it easier to compare individual values.

    ```{r}
    ggplot(data = diamonds) + 
      geom_bar(mapping = aes(x = cut, fill = clarity), position = "dodge") +
      ggtitle('Position = "dodge"')
    ```

***

**Tip** - You can add a title to your plot by adding `+ ggtitle("<Your Title>")` to your plot call.

***

These last type of position adjustment does not make sense for bar charts, but it can be very useful for scatterplots. Recall our first scatterplot. Did you notice that the plot displays only 126 points, even though there are 234 observations in the dataset?

```{r echo = FALSE}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy))
```

The values of `hwy` and `displ` are rounded to the nearest integer and tenths respectively. As a result, the points appear on a grid and many points overlap each other. This arrangement makes it hard to see where the mass of the data is. Are the data points spread equally throughout the graph, or is there one special combination of `hwy` and `displ` that contains 109 values? 

You can avoid this gridding by setting the position adjustment to "jitter".  `position = "jitter"` adds a small amount of random noise to each point. This spreads the points out because no two points are likely to receive the same amount of random noise.

```{r}
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy), position = "jitter") + 
  ggtitle('Position = "jitter"')
```

Adding randomness seems like a strange way to improve your plot, but while makes your graph a less accurate at small scales, it makes your graph _more_ revealing at large scales. Because this is such a useful operation, ggplot2 comes with a shorthand for `geom_point(position = "jitter")`: `geom_jitter()`.

To learn more about a position adjustment, look up the help page associated with each adjustment: `?position_dodge`, `?position_fill`, `?position_identity`, `?position_jitter`, and `?position_stack`.

### Exercises

1.  What is the problem with this plot? How could you improve it?

    ```{r}
    ggplot(data = mpg, mapping = aes(x = cty, y = hwy)) + 
      geom_point()
    ```

1.  Compare and contrast `geom_jitter()` with `geom_count()`.

## Coordinate systems

Coordinate systems are probably the most complicated part of ggplot2. The default coordinate system is the Cartesian coordinate system where the x and y position act independently to find the location of each point.

There are a number of other coordinate systems that are occassionally helpful.

*   `coord_flip()` switches the x and y axes. This is useful (for example),
    if you want vertical boxplots.
    
    ```{r, asp = 1.61}
    ggplot(data = mpg, mapping = aes(x = class, y = hwy)) + 
      geom_boxplot() +
      coord_flip()
    ```

*   `coord_quickmap()` sets the aspect ratio correctly for maps. This is very
    important if you're plotting spatial data with ggplot2 (which unfortunately
    we don't have the space to cover in this book).

    ```{r  fig.width=3, out.width = "50%", fig.align = "default"}
    nz <- map_data("nz")

    ggplot(nz, aes(long, lat, group = group)) +
      geom_polygon(fill = "white", colour = "black")

    ggplot(nz, aes(long, lat, group = group)) +
      geom_polygon(fill = "white", colour = "black") +
      coord_quickmap()
    ```

*   `coord_polar()` uses polar coordinates. Polar coordinates reveals an 
    interesting connection between a bar chart and a Coxcomb chart.
    
    ```{r fig.width=3, out.width = "50%", fig.align = "default"}
    ggplot(data = diamonds) + 
      geom_bar(mapping = aes(x = cut, fill = cut)) + 
      theme(aspect.ratio = 1)
    ggplot(data = diamonds) + 
      geom_bar(mapping = aes(x = cut, fill = cut), width = 1) + 
      coord_polar()
    ```

The table below describes each function and what it does. Add any of these functions to your plot's call to change the coordinate system that the plot uses. You can learn more about each coordinate system by opening its help page in R, e.g. `?coord_cartesian`, `?coord_fixed`, `?coord_flip`, `?coord_map`, `?coord_polar`, and `?coord_trans`.

```{r, echo = FALSE, out.width = "100%"}
knitr::include_graphics("images/visualization-coordinate-systems.png")
```

### Exercises

1.  Turn a stacked bar chart into a pie chart using `coord_polar()`.

1.  What's the difference between `coord_quickmap()` and `coord_map()`?

1.  What does the plot below tell you about the relationship between city
    and highway mpg? Why is `coord_fixed()` important? What does `geom_abline()` 
    do?
    
    ```{r}
    ggplot(data = mpg, mapping = aes(x = cty, y = hwy)) +
      geom_point() + 
      geom_abline() +
      coord_fixed()
    ```

## The layered grammar of graphics

In the previous sections, you learned much more than how to make scatterplots, bar charts, and boxplots. You learned a foundation that you can use to make _any_ type of plot with ggplot2. To see this, lets add position adjustments, stats, coordinate systems, and faceting to our code template:

```
ggplot(data = <DATA>) + 
  <GEOM_FUNCTION>(
     mapping = aes(<MAPPINGS>),
     stat = <STAT>, 
     position = <POSITION>
  ) +
  <COORDINATE_FUNCTION> +
  <FACET_FUNCTION>
```

Our new template takes seven parameters, the bracketed words that appear in the template. In practice, you rarely need to supply all seven parameters to make a graph because ggplot2 will provide useful defaults for everything except the data, the mappings, and the geom function.

The seven parameters in the template compose the grammar of graphics, a formal system for building plots. The grammar of graphics is based on the insight that you can uniquely describe _any_ plot as a combination of a dataset, a geom, a set of mappings, a stat, a position adjustment, a coordinate system, and a faceting scheme. 

To see how this works, consider how you could build a basic plot from scratch: you could start with a dataset and then transform it into the information that you want to display (with a stat).

```{r, echo = FALSE, out.width = "100%"}
knitr::include_graphics("images/visualization-grammar-1.png")
```

Next, you could choose a geometric object to represent each observation in the transformed data. You could then use the aesthetic properties of the geoms to represent variables in the data. You would map the values of each variable to the levels of an aesthetic.

```{r, echo = FALSE, out.width = "100%"}
knitr::include_graphics("images/visualization-grammar-2.png")
```

You'd then select a coordinate system to place the geoms into. You'd use the location of the objects (which is itself an aesthetic property) to display the values of the x and y variables. At that point, you would have a complete graph, but you could further adjust the positions of the geoms within the coordinate system (a position adjustment) or split the graph into subplots (facetting). You could also extend the plot by adding one or more additional layers, where each additional layer uses a dataset, a geom, a set of mappings, a stat, and a position adjustment.

```{r, echo = FALSE, out.width = "100%"}
knitr::include_graphics("images/visualization-grammar-3.png")
```

You could use this method to build _any_ plot that you imagine. In other words, you can use the code template that you've learned in this chapter to build hundreds of thousands of unique plots.