Graphics with R

class: center, middle, inverse, title-slide

.title[
# Graphics with R
]
.author[
### Sara Mortara & Andrea Sánchez-Tapia
]
.institute[
### re.green | ¡liibre!
]
.date[
### 2022-07-13
]

---

## today

- graphics' good practices

- graphics grammar

- examples with `ggplot2`

---
class: middle
## data visualization has many don'ts

.pull-left[
<img src="06_slides_files/figure-html/unnamed-chunk-1-1.png" width="400" style="display: block; margin: auto;" />
]

.pull-right[
<img src="06_slides_files/figure-html/unnamed-chunk-2-1.png" width="400" style="display: block; margin: auto;" />
]

---

## many

.pull-left[
<img src="06_slides_files/figure-html/pie3d-1.png" width="400" style="display: block; margin: auto;" />
]

.pull-right[

]

---
## there's always a better option than a pie chart

.pull-left[

]

.pull-right[

]

---
## barplots are not always very informative

---
## better with error bars...

---
## but maybe don't even make a barplot

---
##  ...or maybe don't even make a graph

---
## make a table

|Treatment| Effect|
|-----------|--------|
|1 |6.7 `\(\pm\)` 0.4 | 
|2 |12.3 `\(\pm\)` 0.98 |

---
## or say it in the text

<center>
The effect of treatment 2 (12.3 ± 0.98) was
higher than treatment 1 (6.7 ± 0.4).

---
## do not fool your reader

[Free range statistics](http://freerangestats.info/blog/2020/04/06/crazy-fox-y-axis)

---
## do not fool your reader

[Free range statistics](http://freerangestats.info/blog/2020/04/06/crazy-fox-y-axis)

---
## some basic tips in general

+ only make plots when you really need to

+ don't spend more ink and colors than you need to

+ don't fool your reader (no y-axis tampering, no undue transformation)

+ show error measures

---
## some basic tips in R

+ make your y-axis labels horizontal and visible

+ avoid colored backgrounds

+ use dots for scatterplots

+ add names to `xlab` and `ylab`

+ save to png and pdf formats

---

## the grammar of graphics

.pull-left[
- a theoretical deconstruction for data graphics

- foundation for software (ggplot2, [vega-lite](https://vega.github.io/vega-lite/))

- how to design the system that allow building beautiful, correct graphics
]

.pull-right[

]

---
background-image: url("figs/logo.png")
background-position: 98% 2%
background-size: 100px

## the grammar of graphics: ggplot2

Hadley Wickham, Danielle Navarro, and Thomas Lin Pedersen

.pull-left[

- [https://ggplot2-book.org/](https://ggplot2-book.org/)

- not a cookbook ([R Graphics Cookbook, Winston Chang](https://r-graphics.org/))

- underlying theory

- power to tailor any plot

]

.pull-right[
<img src="figs/book.jpg" width="200" style="display: block; margin: auto;" />

]

---

## graphics

Type of graphic | R base | 
----------|------------|
barplot | barplot() | 
histogram | histogram() | 
density | plot(density()) | 
quantile-quantile |	qqnorm()	| 
boxplot | boxplot() | 
scatterplot | plot() |

---
## grammar: decompose graphics into its constituints

- theme
- coordinates
- facets
- geometries
- scales
- statistics
- mapping
- data
    - it will require data in a variable/colum observation/row format

---
class: inverse, middle, center

background-image: url("figs/logo.png")
background-position: 98% 2%
background-size: 100px/

## ggplot2

---

## barplot

- ToothGrowth data sets
- the effect of Vitamin C on Tooth growth in Guinea pigs
- len: Tooth length
- dose: Dose in milligrams (0.5, 1, 2)

.tiny[

```r
library(ggplot2)

df <- data.frame(dose = c("D0.5", "D1", "D2"),
                 len = c(4.2, 10, 29.5))
df
```

```
##   dose  len
## 1 D0.5  4.2
## 2   D1 10.0
## 3   D2 29.5
```

]

---
## create a barplot

.tiny[

```r
bar1 <- ggplot(data = df, mapping = aes(x = dose, y = len)) +
  geom_bar(stat = "identity")
bar1
```

]

---
## create a barplot

.tiny[

```r
# Data and mapping can be given both as global (in ggplot()) or per layer
bar1 <- ggplot() +
  geom_bar(data = df, mapping = aes(x = dose, y = len), 
           stat = "identity")
bar1
```

]

---
## create a horizontal barplot

```r
bar1 + coord_flip()
```

---

## change the bar color

```r
ggplot(data = df, mapping = aes(x = dose, y = len)) +
  geom_bar(stat = "identity", fill = "red")
```

---

## change the bar color using the hexcode

```r
ggplot(data = df, mapping = aes(x = dose, y = len)) +
  geom_bar(stat = "identity", fill = "#A70000")
```

---
## changing the theme

.tiny[

```r
ggplot(data = df, mapping = aes(x = dose, y = len)) +
  geom_bar(stat = "identity", fill = "#A70000") + 
  theme_classic()
```

]

---
## defining a parameters for a theme

```r
title_size <- 18
text_size <- 16
my_theme <- theme_classic() +
  theme(axis.title.x = element_text(size = title_size),
        axis.text.x = element_text(size = text_size),
        axis.title.y = element_text(size = title_size),
        axis.text.y = element_text(size = text_size))
```

---
## changing labels and size

.tiny[

```r
ggplot(data = df, mapping = aes(x = dose, y = len)) +
  geom_bar(stat = "identity", fill = "#A70000") + 
  labs(x = "Dose", y = "Tooth length (cm)") +
  my_theme
```

]

---
## do we need color?

.tiny[

```r
ggplot(data = df, aes(x = dose, y = len, fill = dose)) +
  geom_bar(stat = "identity") + 
  labs(x = "Dose", y = "Tooth length (cm)") +
  scale_fill_manual(values = c("#E69F00", "#56B4E9", "#CC79A7")) +
  my_theme
```

]

---
## barplot with subcategories

Adding with each of two delivery methods: 
- orange juice (OJ)
- ascorbic acid (VC)

.tiny[

```r
df2 <- data.frame(supp = rep(c("VC", "OJ"), each = 3),
                  dose = rep(c("D0.5", "D1", "D2"), 2),
                  len = c(6.8, 15, 33, 4.2, 10, 29.5))
head(df2)
```

```
##   supp dose  len
## 1   VC D0.5  6.8
## 2   VC   D1 15.0
## 3   VC   D2 33.0
## 4   OJ D0.5  4.2
## 5   OJ   D1 10.0
## 6   OJ   D2 29.5
```
]

---
## barplot with subcategories

.tiny[

```r
ggplot(data = df2, aes(x = dose, y = len, fill = supp)) +
  geom_bar(stat = "identity") +
  scale_fill_brewer(palette = "Paired") +
  my_theme
```

]

---
## scatterplot

.tiny[

```r
data("faithful")
# Basic scatterplot
ggplot(data = faithful, 
       mapping = aes(x = eruptions, y = waiting)) + 
  geom_point() + my_theme
```

<img src="06_slides_files/figure-html/unnamed-chunk-24-1.png" width="400" style="display: block; margin: auto;" />
]

---

## scatterplot

.tiny[

```r
# Data and mapping can be given both as global (in ggplot()) or per layer
ggplot() + 
  geom_point(mapping = aes(x = eruptions, y = waiting),
             data = faithful) + my_theme
```

<img src="06_slides_files/figure-html/unnamed-chunk-25-1.png" width="400" style="display: block; margin: auto;" />
]

---

## aesthetic linked to data aes()

.tiny[

```r
ggplot(faithful) + 
  geom_point(aes(x = eruptions, y = waiting, colour = eruptions < 3)) +
  my_theme
```

<img src="06_slides_files/figure-html/unnamed-chunk-26-1.png" width="400" style="display: block; margin: auto;" />
]

---
## set color to a value outside `aes()`

.tiny[

```r
ggplot(faithful) + 
  geom_point(aes(x = eruptions, y = waiting),
             colour = 'steelblue') + 
  my_theme
```

<img src="06_slides_files/figure-html/unnamed-chunk-27-1.png" width="400" style="display: block; margin: auto;" />
]

---
## histogram

.tiny[

```r
ggplot(faithful) + 
  geom_histogram(aes(x = eruptions), bins = 40) +
  my_theme
```

<img src="06_slides_files/figure-html/unnamed-chunk-28-1.png" width="400" style="display: block; margin: auto;" />
]

---
## scales

.tiny[

```r
ggplot(mpg) + 
  geom_point(aes(x = displ, y = hwy)) + 
  scale_x_continuous(breaks = c(3, 5, 6)) + 
  scale_y_continuous(trans = 'log10') +
  my_theme
```

]

---
## facets

.tiny[

```r
ggplot(mpg) + 
  geom_point(aes(x = displ, y = hwy)) + 
  facet_wrap(~ class) + my_theme
```

]

---
## facets

.tiny[

```r
ggplot(mpg) + 
  geom_point(aes(x = displ, y = hwy)) + 
  facet_grid(year ~ drv) + my_theme
```

]

---

### plot composition

.tiny[

```r
msleep <- na.omit(msleep)
p1 <- ggplot(msleep) + 
  geom_boxplot(aes(x = sleep_total, y = vore, fill = vore)) +
  my_theme
p1 
```

<img src="06_slides_files/figure-html/unnamed-chunk-32-1.png" width="400" style="display: block; margin: auto;" />
]

---
## plot composition

.tiny[

```r
p2 <- ggplot(msleep) + 
  geom_bar(aes(y = vore, fill = vore)) +
  my_theme
p2
```

<img src="06_slides_files/figure-html/unnamed-chunk-33-1.png" width="400" style="display: block; margin: auto;" />
]

---
## plot composition

.tiny[

```r
p3 <- ggplot(msleep) + 
  geom_point(aes(x = bodywt, y = sleep_total, colour = vore)) + 
  scale_x_log10() +
  my_theme
p3
```

]

---
## patchwork

```r
library(patchwork)
p1 + p2 + p3
```

---
## patchwork

.tiny[

```r
(p1 | p2) / p3 + plot_layout(guides = 'collect') + 
  plot_annotation(title = 'Mammalian sleep patterns',
                  tag_levels = 'A')
```

<img src="06_slides_files/figure-html/unnamed-chunk-36-1.png" width="400" style="display: block; margin: auto;" />
]

---
## density ridges

.tiny[

```r
library(ggridges)
df_diamonds <- diamonds[1:100, c("color", "depth")]
ggplot(df_diamonds, aes(x = depth, y = color)) +
  geom_density_ridges() + my_theme
```

]

---
## other resources

.pull-left[
- color palletes:
  - [Color Brewer](http://colorbrewer2.org/)
  - [Adobe Color ](https://color.adobe.com/create)
  - [COLOR lovers](https://www.colourlovers.com/)
  
- icons for graphics:
  - [The noun project](https://thenounproject.com/)
  - [iconmonst](https://iconmonstr.com/)
]

.pull-right[
- R packges:
  - `wesanderson`
  - `RColorBrewer`
  - `swatches`
  - `colourlovers`
]

---
class: inverse, middle, center

# aRt

---

useR!2021

---

useR!2021

---
## todo

- create and run `Rmd` file `graphics.Rmd`

- `git add`, `commit`, and `push` of the day

---
class: center, middle

# ¡Thanks!

<center>
<svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:#A70000;height:1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M476 3.2L12.5 270.6c-18.1 10.4-15.8 35.6 2.2 43.2L121 358.4l287.3-253.2c5.5-4.9 13.3 2.6 8.6 8.3L176 407v80.5c0 23.6 28.5 32.9 42.5 15.8L282 426l124.6 52.2c14.2 6 30.4-2.9 33-18.2l72-432C515 7.8 493.3-6.8 476 3.2z"></path></svg> [saramortara@gmail.com](mailto:saramortara@gmail.com) | [andreasancheztapia@gmail.com](mailto:andreasancheztapia@gmail.com)