ggplot Part I

.title[
# ggplot Part I
]
.subtitle[
## SBW - Data Visualization Workshop
]
.author[
### Lokesh Mano • 28-Oct-2022
]
.institute[
### NBIS, SciLifeLab
]

---

---

## Contents

* [Grammer of Graphics](#gog)
* [Building a graph](#build)
* [Build-Demo](#build-demo)
* [Geoms](#geoms)
* [Aesthetics](#aesth)
* [Multiple Geoms](#mul-geom)
* [Scales - color](#scales-discrete-color)
* [Scales - shape](#scales-shape)
* [facet_wrap](#facet-wrap)

---

## Grammar of Graphics

.pull-right-70[
* **Data:** Input data
* **Geom:** A geometry representing data. Points, Lines etc
* **Aesthetics:** Visual characteristics of the geometry. Size, Color, Shape etc
* **Scale:** How visual characteristics are converted to display values
* **Statistics:** Statistical transformations. Counts, Means etc
* **Coordinates:** Numeric system to determine position of geometry. Cartesian, Polar etc
* **Facets:** Split data into subsets
]

---

## Building a graph

---

## Build-Demo

```r
ggplot(iris)
```
]

.pull-right-50[
<img src="slide_gg1_files/figure-html/unnamed-chunk-4-1.svg" style="display: block; margin: auto auto auto 0;" />
]

---

## Build-Demo

```r
ggplot(iris,aes(x=Sepal.Length,
                y=Sepal.Width))
```
]

.pull-right-50[
<img src="slide_gg1_files/figure-html/unnamed-chunk-6-1.svg" style="display: block; margin: auto auto auto 0;" />
]

---

## Build-Demo

```r
ggplot(iris,aes(x=Sepal.Length,
                y=Sepal.Width))+
  geom_point()
```
]

.pull-right-50[
<img src="slide_gg1_files/figure-html/unnamed-chunk-8-1.svg" style="display: block; margin: auto auto auto 0;" />
]

---

## Build-Demo

```r
ggplot(iris,aes(x=Sepal.Length,
                y=Sepal.Width,
                colour=Species))+
  geom_point()
```
]

.pull-right-50[
<img src="slide_gg1_files/figure-html/unnamed-chunk-10-1.svg" style="display: block; margin: auto auto auto 0;" />
]

---

## Geoms

```r
p <- ggplot(iris)
# scatterplot
p+geom_point(aes(x=Sepal.Length,y=Sepal.Width))
# barplot
p+geom_bar(aes(x=Sepal.Length))
# boxplot
p+geom_boxplot(aes(x=Species,y=Sepal.Width))
# search
help.search("^geom_",package="ggplot2")
```

---

## Aesthetics

* Aesthetic mapping vs aesthetic parameter

```r
ggplot(iris)+
  geom_point(aes(x=Sepal.Length,
                 y=Sepal.Width,
                 size=Petal.Length,
                 alpha=Petal.Width,
                 shape=Species,
                 color=Species))
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-12-1.svg" style="display: block; margin: auto auto auto 0;" />
]

```r
ggplot(iris)+
  geom_point(aes(x=Sepal.Length,
                 y=Sepal.Width),
                 size=2,
                 alpha=0.8,
                 shape=15,
                 color="steelblue")
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-13-1.svg" style="display: block; margin: auto auto auto 0;" />
]

---

## Multiple geoms

```r
ggplot(iris,aes(x=Sepal.Length,y=Sepal.Width))+
      geom_point()+
      geom_line()+
      geom_smooth()+
      geom_rug()+
      geom_step()+
      geom_text(data=subset(iris,iris$Species=="setosa"),aes(label=Species))
```

---

## Scales • Discrete Colors

* scales: position, color, fill, size, shape, alpha, linetype
* syntax: `scale_<aesthetic>_<type>`

```r
p <- ggplot(iris)+geom_point(aes(x=Sepal.Length,
 y=Sepal.Width,color=Species))
p
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-15-1.svg" style="display: block; margin: auto auto auto 0;" />
]

```r
p + scale_color_manual(
     name="Manual",
     values=c("#5BC0EB","#FDE74C","#9BC53D"))
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-16-1.svg" style="display: block; margin: auto auto auto 0;" />
]

---

## Scales • Continuous Colors

* In RStudio, type `scale_`, then press **TAB**

```r
p <- ggplot(iris)+
 geom_point(aes(x=Sepal.Length,
 y=Sepal.Width,
 shape=Species,color=Petal.Length))
p
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-17-1.svg" style="display: block; margin: auto auto auto 0;" />
]

```r
p + 
scale_color_gradient(name="Pet Len",
  breaks=range(iris$Petal.Length),
  labels=c("Min","Max"),
  low="black",high="red")
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-18-1.svg" style="display: block; margin: auto auto auto 0;" />
]

---

## Scales • Shape

```r
p <- ggplot(iris)+
 geom_point(aes(x=Sepal.Length,
 y=Sepal.Width,
 shape=Species,color=Species))
p
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-19-1.svg" style="display: block; margin: auto auto auto 0;" />
]

```r
p + 
scale_color_manual(name="New",
   values=c("blue","green","red"))+
scale_shape_manual(name="Bla",values=c(0,1,2))
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-20-1.svg" style="display: block; margin: auto auto auto 0;" />
]

---

## Facets • `facet_wrap`

* Split to subplots based on variable(s)
* Facetting in one dimension

```r
p <- ggplot(iris)+
 geom_point(aes(x=Sepal.Length,
 y=Sepal.Width,
 color=Species))
p
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-21-1.svg" style="display: block; margin: auto auto auto 0;" />
]

```r
p + facet_wrap(~Species)
```

```r
p + facet_wrap(~Species,nrow=3)
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-23-1.svg" style="display: block; margin: auto auto auto 0;" />
]

---

## Facets • `facet_grid`

* Facetting in two dimensions

```r
p <- diamonds %>%
 ggplot(aes(carat,price))+
 geom_point()
p + facet_grid(~cut+clarity)
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-24-1.svg" style="display: block; margin: auto auto auto 0;" />
]

```r
p + facet_grid(cut~clarity)
```

<img src="slide_gg1_files/figure-html/unnamed-chunk-25-1.svg" style="display: block; margin: auto auto auto 0;" />
]

---

# Thank you. Questions?

<hr>

Built on : 28-Oct-2022 at 07:32:28

2022 • [SciLifeLab](https://www.scilifelab.se/) • [NBIS](https://nbis.se/)
]