---
title: Annotating a plot
author: Abhijit Dasgupta, PhD
---

```{r setup, include=FALSE, child = here::here('slides/templates/setup.Rmd')}
```

```{r setup1, include=FALSE}
setwd(here::here('slides/lectures'))
library(tidyverse)
theme_set(theme_classic()+theme(axis.text = element_text(size=14),
                                axis.title = element_text(size=16),
                                legend.text = element_text(size=14),
                                legend.title = element_text(size=16),
                                plot.title = element_text(size=18),
                                plot.subtitle = element_text(size=16),
                                plot.caption = element_text(size=12)))
```

layout: true

<div class="my-header">
<span>BIOF 339: Practical R</span></div>

---
class:middle, center, inverse

# Annotations

---

## Stand-alone stories

- You would like a data visualization to stand on its own
- Relevant information should be placed on the graph
- However, you need to balance the information content with real estate
    - Don't clutter the graph and make it not readable

---


## An example 

<div id="origecon"></div>
![](img/economist1.gif)

We will recreate this plot in a tutorial

---

## Titles, subtitles and captions

.pull-left[
```{r p1, eval = F, echo = T}
library(palmerpenguins)
(plt <- ggplot(penguins, 
               aes(bill_length_mm, body_mass_g, 
                   color=species))+
  geom_point())
```
]
.pull-right[
```{r, eval=T, echo = F, ref.label="p1"}
```
]



---

## Titles, subtitles and captions

.pull-left[
```{r p2, eval = F, echo = T}
library(palmerpenguins)
plt <- ggplot(penguins, 
              aes(bill_length_mm, body_mass_g, 
                  color=species))+
  geom_point()
plt + 
  labs(x = 'Bill length (mm)',
       y = 'Body mass (g)')
```
]
.pull-right[
```{r, eval=T, echo = F, ref.label="p2"}
```
]


---

## Titles, subtitles and captions


.pull-left[
```{r p3, eval = F, echo = T}
library(palmerpenguins)
plt <- ggplot(penguins, 
              aes(bill_length_mm, body_mass_g, 
                  color=species))+
  geom_point()
plt + 
  labs(x = 'Bill length (mm)',
       y = 'Body mass (g)',
       color = 'Species') #<<
```
]
.pull-right[
```{r, eval=T, echo = F, ref.label="p3"}
```
]

---

## Titles, subtitles and captions


.pull-left[
```{r p4, eval = F, echo = T}
library(palmerpenguins)
plt <- ggplot(penguins, 
              aes(bill_length_mm, body_mass_g, 
                  color=species))+
  geom_point()
plt + 
  labs(x = 'Bill length (mm)',
       y = 'Body mass (g)',
       color = 'Species',
       title = "Palmer penguins",#<<
       subtitle = "Bill length vs Body mass") #<<
```
]
.pull-right[
```{r, eval=T, echo = F, ref.label="p4"}
```
]

---

## Titles, subtitles and captions


.pull-left[
```{r p5, eval = F, echo = T}
library(palmerpenguins)
plt <- ggplot(penguins, 
              aes(bill_length_mm, body_mass_g, 
                  color=species))+
  geom_point()
plt + 
  labs(x = 'Bill length (mm)',
       y = 'Body mass (g)',
       color = 'Species',
       title = "Palmer penguins",
       subtitle = "Bill length vs Body mass",
       caption = "Palmer Station LTER") 
```
]
.pull-right[
```{r, eval=T, echo = F, ref.label="p5"}
```
]
---
class:middle,center

# Adding derived statistics to a plot

---

## Adding group means

.pull-left[
```{r b1, eval = F, echo = T}
ggplot(penguins, 
       aes(x = bill_length_mm,
           y = body_mass_g,
           color = species))+
  geom_point()
```
]
.pull-right[
```{r, eval=T, echo=F, ref.label="b1"}

```

]

---

## Adding group means

.pull-left[
```{r 05-Lecture5-11, eval = T, echo = T}
means <- penguins %>% group_by(species) %>% 
  summarize_at(vars(bill_length_mm, body_mass_g),
               mean, na.rm=TRUE)
means
```


```{r b2, eval = F, echo = T}
ggplot(penguins, 
       aes(x = bill_length_mm,
           y = body_mass_g,
           color = species))+
  geom_point()+ 
  geom_point(data = means, #<<
             size=8) #<<
```

Adding data from a different dataset

]
.pull-right[
```{r, eval=T, echo=F, ref.label='b2'}

```

]
---



## Adding regression metrics

.pull-left[

Regress highway mileage on city mileage (data: mpg)

```{r c1, eval = F, echo = T}
mod1 <- lm(hwy ~ cty, data = mpg)
r2 <- broom::glance(mod1) %>% pull(r.squared)

ggplot(mpg, 
       aes(x = cty, y = hwy))+
  geom_point() + 
  geom_smooth(method = 'lm', se=F) +
  theme_bw()
```
]
.pull-right[
```{r,eval=T, echo=F, ref.label='c1'}

```
]
---

## Adding regression metrics

.pull-left[

Regress highway mileage on city mileage (data: mpg)

```{r c2, eval = F, echo = T}
mod1 <- lm(hwy ~ cty, data = mpg)
r2 <- broom::glance(mod1) %>% pull(r.squared) %>% 
  round(., 2)

ggplot(mpg, 
       aes(x = cty, y = hwy))+
  geom_point() + 
  geom_smooth(method = 'lm', se=F)+
  annotate(geom='text',
           x = 15, y = 40,
           label=glue::glue("R^2 == {r}",r=r2),
           size=12,
           parse=T) + 
  theme_bw()
```
]
.pull-right[
```{r, eval=T, echo=F, ref.label='c2'}

```

]

---

## Highlighting regions

.pull-left[
```{r d1, eval = F, echo = T}
mpg %>% 
  mutate(cyl = as.factor(cyl)) %>% 
  ggplot(aes(x = cyl, y = hwy)) + 
  geom_boxplot() + 
  theme_bw()
```
]
.pull-right[
```{r, eval=T, echo=F, ref.label='d1'}

```

]

---

## Highlighting regions

.pull-left[
```{r d2, eval = F, echo = T}
mpg %>% 
  mutate(cyl = as.factor(cyl)) %>% 
  ggplot(aes(x = cyl, y = hwy)) + 
  geom_boxplot() + 
  theme_bw()+
  annotate(geom = 'rect',
           xmin=3.75,xmax=4.25,
           ymin = 22, ymax = 28,
           fill = 'red',
           alpha = 0.2) +
  annotate('text', 
           x = 4.5, y = 25,
           label = 'Outliers?',
           hjust = 0)+
  coord_cartesian(xlim = c(0,5))+ 
  theme_bw()
```

Note: If you have a factor on the x-axis, they are plotted at 1, 2, 3, ...
]
.pull-right[
```{r, eval=T, echo=F, ref.label='d2'}

```

]