ggplot Part III

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# ggplot Part III
## Workshop on Plotting in R
### Lokesh Mano • 18-Jan-2022
### NBIS, SciLifeLab

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class: spaced

## Contents

* [Scales - axis](#scales-axis)
* [Coordinate Systems](#coordinate)
* [Theme](#theme)
* [Theme - Legend](#theme-legend)
* [Theme - Text](#theme-text)
* [Theme - Rect](#theme-rect)
* [Theme - Reuse](#theme-reuse)

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name: scales-axis

## Scales • Axes

* scales: x, y
* syntax: `scale_<axis>_<type>`
* arguments: name, limits, breaks, labels

.pull-left-50[

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

<img src="slide_gg3_files/figure-html/unnamed-chunk-3-1.svg" style="display: block; margin: auto auto auto 0;" />
]

.pull-right-50[

```r
p + scale_color_manual(name="New",
   values=c("blue","green","red"))+
scale_x_continuous(name="Sepal Length",
        breaks=seq(1,8),limits=c(3,5))
```

<img src="slide_gg3_files/figure-html/unnamed-chunk-4-1.svg" style="display: block; margin: auto auto auto 0;" />
]
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name: coordinate

## Coordinate Systems

![](assets/images/coordinate.png)

* `coord_cartesian(xlim=c(2,8))` for zooming in
* `coord_map` for controlling limits on maps
* `coord_polar`

.pull-left-50[

```r
p <- ggplot(iris,aes(x="",y=Petal.Length,fill=Species))+
 geom_bar(stat="identity")
p
```

<img src="slide_gg3_files/figure-html/unnamed-chunk-5-1.svg" style="display: block; margin: auto auto auto 0;" />
]

???

The coordinate system defines the surface used to represent numbers. Most plots use the cartesian coordinate sytem. Pie charts for example, is a polar coordinate projection of a cartesian barplot. Maps for example can have numerous coordinate systems called map projections. For example; UTM coordinates.

.pull-right-50[

```r
p+coord_polar("y",start=0)
```

<img src="slide_gg3_files/figure-html/unnamed-chunk-6-1.svg" style="display: block; margin: auto auto auto 0;" />
]

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name: theme

## Theme

* Modify non-data plot elements/appearance
* Axis labels, panel colors, legend appearance etc
* Save a particular appearance for reuse
* `?theme`

.pull-left-50[

```r
ggplot(iris,aes(Petal.Length))+
  geom_histogram()+
  facet_wrap(~Species,nrow=2)+
  theme_grey()
```

<img src="slide_gg3_files/figure-html/unnamed-chunk-7-1.svg" style="display: block; margin: auto auto auto 0;" />
]

.pull-right-50[

```r
ggplot(iris,aes(Petal.Length))+
  geom_histogram()+
  facet_wrap(~Species,nrow=2)+
  theme_bw()
```

<img src="slide_gg3_files/figure-html/unnamed-chunk-8-1.svg" style="display: block; margin: auto auto auto 0;" />
]

???

Themes allow to modify all non-data related components of the plot. This is the visual appearance of the plot. Examples include the axes line thickness, the background color or font family.

---
name: theme-legend

## Theme • Legend

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

.pull-left-50[

```r
p + theme(legend.position="top")
```

<img src="slide_gg3_files/figure-html/unnamed-chunk-10-1.svg" style="display: block; margin: auto auto auto 0;" />
]

.pull-right-50[

```r
p + theme(legend.position="bottom")
```

<img src="slide_gg3_files/figure-html/unnamed-chunk-11-1.svg" style="display: block; margin: auto auto auto 0;" />
]

---
name: theme-text

## Theme • Text

```r
element_text(family=NULL,face=NULL,color=NULL,size=NULL,hjust=NULL,
             vjust=NULL, angle=NULL,lineheight=NULL,margin = NULL)
```

```r
p <- p + theme(
 axis.title=element_text(color="#e41a1c"),
 axis.text=element_text(color="#377eb8"),
 plot.title=element_text(color="#4daf4a"),
 plot.subtitle=element_text(color="#984ea3"),
 legend.text=element_text(color="#ff7f00"),
 legend.title=element_text(color="#ffff33"),
 strip.text=element_text(color="#a65628")
)
```

---
name: theme-rect

## Theme • Rect

```r
element_rect(fill=NULL,color=NULL,size=NULL,linetype=NULL)
```

```r
p <- p + theme(
 plot.background=element_rect(fill="#b3e2cd"),
 panel.background=element_rect(fill="#fdcdac"),
 panel.border=element_rect(fill=NA,color="#cbd5e8",size=3),
 legend.background=element_rect(fill="#f4cae4"),
 legend.box.background=element_rect(fill="#e6f5c9"),
 strip.background=element_rect(fill="#fff2ae")
)
```

---
name: theme-reuse

## Theme • Reuse

```r
newtheme <- theme_bw() + theme(
 axis.ticks=element_blank(),
 panel.background=element_rect(fill="white"),
 panel.grid.minor=element_blank(),
 panel.grid.major.x=element_blank(),
 panel.grid.major.y=element_line(size=0.3,color="grey90"),
 panel.border=element_blank(),
 legend.position="top",
 legend.justification="right"
)
```

.pull-left-50[

```r
p
```

<img src="slide_gg3_files/figure-html/unnamed-chunk-22-1.svg" style="display: block; margin: auto auto auto 0;" />
]

.pull-right-50[

```r
p + newtheme
```

<img src="slide_gg3_files/figure-html/unnamed-chunk-23-1.svg" style="display: block; margin: auto auto auto 0;" />
]

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# Thank you. Questions?

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R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit)OS: Ubuntu 18.04.6 LTS

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Built on : 18-Jan-2022 at 09:51:16

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