viz_slides.utf8

class: center, middle, inverse, title-slide

# <div class="line-block">Getting Started in R<br />
an introduction to data analysis and visualisation</div>
## Visualising Data
### Réka Solymosi, Sam Langton & Emily Buehler
### 4 July 2019

---

class: inverse, center, middle

# Data viz

---
### The grammar of graphics

![](img/gg1.png)

[Wickham, H. (2010). A layered grammar of graphics. Journal of Computational and Graphical Statistics, 19(1), 3-28.](http://vita.had.co.nz/papers/layered-grammar.pdf)

---
### The grammar of graphics

![](img/gg2.png)

[Wickham, H. (2010). A layered grammar of graphics. Journal of Computational and Graphical Statistics, 19(1), 3-28.](http://vita.had.co.nz/papers/layered-grammar.pdf)

---
### The grammar of graphics

![](img/gg3.png)

[Wickham, H. (2010). A layered grammar of graphics. Journal of Computational and Graphical Statistics, 19(1), 3-28.](http://vita.had.co.nz/papers/layered-grammar.pdf)

---
### The grammar of graphics

![](img/layers.png)

[Wickham, H. (2010). A layered grammar of graphics. Journal of Computational and Graphical Statistics, 19(1), 3-28.](http://vita.had.co.nz/papers/layered-grammar.pdf)

---
### The grammar of graphics

![](img/combined.png)

[Wickham, H. (2010). A layered grammar of graphics. Journal of Computational and Graphical Statistics, 19(1), 3-28.](http://vita.had.co.nz/papers/layered-grammar.pdf)

---

### The grammar of graphics

![](https://www.science-craft.com/wp-content/uploads/2014/06/ggplot-1.png)

---
### Creating a ggplot

```r
library(ggplot2)
```

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

<img src="viz_slides_files/figure-html/unnamed-chunk-2-1.png" height="400px" />

---
### Pseudocode

```r
ggplot(data = <DATA>) + 
  <GEOM_FUNCTION>(mapping = aes(<MAPPINGS>))
```

---
### 3 variables to 1 plot: `colour =`

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

<img src="viz_slides_files/figure-html/unnamed-chunk-4-1.png" height="400px" />

---
### 3 variables to 1 plot: `size =`

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

```
## Warning: Using size for a discrete variable is not advised.
```

<img src="viz_slides_files/figure-html/unnamed-chunk-5-1.png" height="400px" />

---
### 3 variables to 1 plot: `shape =`

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

```
## Warning: The shape palette can deal with a maximum of 6 discrete values
## because more than 6 becomes difficult to discriminate; you have 7.
## Consider specifying shapes manually if you must have them.
```

```
## Warning: Removed 62 rows containing missing values (geom_point).
```

<img src="viz_slides_files/figure-html/unnamed-chunk-6-1.png" height="330px" />

---
### 3 variables to 1 plot: `facet_wrap()`

```r
ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy)) + 
  facet_wrap(~ class, nrow = 2)
```

<img src="viz_slides_files/figure-html/unnamed-chunk-7-1.png" height="400px" />

---
### Geoms

How are these two plots similar?

<img src="http://r4ds.had.co.nz/visualize_files/figure-html/unnamed-chunk-18-1.png" width="400px" /><img src="http://r4ds.had.co.nz/visualize_files/figure-html/unnamed-chunk-18-2.png" width="400px" />

---
### Geoms

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

<img src="viz_slides_files/figure-html/unnamed-chunk-9-1.png" height="400px" />

---
### Geoms ++

![](https://www.rstudio.com/wp-content/uploads/2016/11/ggplot2-cheatsheet-2-1.png)
---

### Geoms ++

[Online companions](https://www.trafforddatalab.io/graphics_companion/)

![](img/gg_online.png)

---

### Making this plot

![](viz_slides_files/figure-html/unnamed-chunk-10-1.png)

---

### Data + aesthetics + geom

```r
bp <- ggplot(data = PlantGrowth) +
  geom_boxplot(mapping = aes(x = group, y = weight))
bp
```

---

### Initial tweaks

```r
bp <- ggplot(data = PlantGrowth) +
  geom_boxplot(mapping = aes(x = group, y = weight, fill = group),
               size = 1.2, alpha = 0.8)
bp
```

---

### Axes

```r
bp + scale_x_discrete(labels = c("control", "treat1", "treat2"))
```

```r
# Hide x tick marks, labels, and grid lines
bp + scale_x_discrete(breaks=NULL) 
```

---

### Labels

```r
bp + labs(title = "Figure 1: group distributions", x = " ")
```

---

### Colour brewers

```r
bp + scale_fill_brewer(palette = "Accent")
```

---

### Themes

```r
bp + theme_minimal()
```

---

### Themes (specific options)

```r
bp + theme(legend.position = "none",
        axis.text.x = element_text(color="#707070",
                                   size=12),
        axis.title.x = element_text(size = 14),
        axis.text.y = element_text(color="#707070",
                                   size=10,
                                   angle=45))
```

---

### Making this plot

```r
bp <- ggplot(data = PlantGrowth) +
  geom_boxplot(mapping = aes(x = group, y = weight, fill = group),
               size = 1.2, alpha = 0.8) +
  scale_x_discrete(labels = c("control", "treat1", "treat2")) +
  labs(title = "Figure 1: group distributions",
         x = " ") +
  scale_fill_brewer(palette = "Accent") +
  theme_minimal() +
  theme(legend.position = "none",
        plot.title = element_text(size=18),
        axis.text.x  = element_text(color="#707070",
                                   size=12),
        axis.title.y = element_text(size=16),
        axis.text.y  = element_text(color="#707070",
                                   size=10,
                                   angle=45))
bp
```

---

### Making this plot interactive

```r
ggplotly(bp)
```

---

### Making this plot interactive

<div id="htmlwidget-f13d8997168f315df98f" style="width:504px;height:504px;" class="plotly html-widget"></div>
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---
###Rcolorbrewer

[Sequential, diverging and qualitative colour scales from colorbrewer.org](http://ggplot2.tidyverse.org/reference/scale_brewer.html)

&

[Colour summaries from http://www.cookbook-r.com](http://www.cookbook-r.com/Graphs/Colors_(ggplot2))

![](img/gg_colours.png)

---

### It's all the same!

![](img/gg_examples.png)