Computing in R

class: center, middle, inverse, title-slide

.title[
# Computing in R
]
.subtitle[
## Amsterdam UMC Doctoral School
]
.author[
### Perry Moerland
]
.date[
### 9-13 December 2024
]

---

# Graphics

R has versatile tools for graphics. There are typically three steps to
producing useful graphics:

1. Creating the basic plot

1. Enhancing the plot with labels, legends, colors etc.

1. Exporting the plot from R for use elsewhere
  
---
# Basic plot (I)

It is straightforward to make a simple plot using functions from the
__graphics__ package (loaded by default):

``` r
> x <- (0:100)/10
> plot(x, x^3 - 13 * x^2 + 39 * x)
```

![](data:image/png;base64,#Figures/poly1-1.svg)
---
# Basic plot (II)
You can increase the size of the symbols on the axes and the axis labels (_cex_ stands for character expansion factor):

``` r
> plot(x, x^3 - 13 * x^2 + 39 * x,cex.axis=1.3,cex.lab=1.5)
```

![](data:image/png;base64,#Figures/poly2-1.svg)

---
# Basic plot (III)

Change the type of plot via the argument _type_: "p" for points (is default), "l" for lines, etc. See [?plot](https://www.rdocumentation.org/packages/graphics/versions/3.5.1/topics/plot) for other options

``` r
> plot(x,x^3-13*x^2+39*x,type="l",cex.axis=1.3,cex.lab=1.5)
```

![](data:image/png;base64,#Figures/poly3-1.svg)

---
# Basic plot (IV)

- Change the titles for the axes via _xlab_ and _ylab_
- Add an overall title for the plot via _main_

``` r
> plot(x,x^3-13*x^2+39*x,type="l",xlab="time (hours)",
+      ylab="temperature",main="Enhanced plot",cex.axis=1.3,
+      cex.lab=1.5)
```

![](data:image/png;base64,#Figures/poly4-1.svg)
---
# Basic plot (V)
- Change the plot symbol used from the default dot using the argument _pch_ (see [reference card](http://bioinformaticslaboratory.eu/wp-content/uploads/gs-computing-in-r/R-refcard-v2.pdf))
- Change the colour via the argument _col_. By name: see `colors()` for the 657 [options](https://rstudio-pubs-static.s3.amazonaws.com/3486_79191ad32cf74955b4502b8530aad627.html). By number: see `palette()`

``` r
> plot(x,x^3-13*x^2+39*x,pch=18,xlab="time (hours)",
+      ylab="temperature",col="red",main="Enhanced plot",
+      cex.axis=1.3,cex.lab=1.5)
```

![](data:image/png;base64,#Figures/poly5-1.svg)

---
# Plot symbols

There are 25 different plot symbols, see [?points](https://www.rdocumentation.org/packages/graphics/versions/3.5.1/topics/points)

``` r
> plot(1:25, pch=1:25,cex=2,bg="grey")
> # bg: background colors for open plot symbols
```

![](data:image/png;base64,#Figures/pch-1.svg)

---
# Enhancing a plot

.pull-left[

``` r
x<-(0:100)/10
plot(x,x^3-13*x^2+39*x,
     type="l",
     xlab="time (hours)",
     ylab="temperature",
     cex.axis=1.5,cex.lab=1.5)
```
]

.pull-right[
![](data:image/png;base64,#Figures/stepwise-plot1-1.png)
]

---
# Enhancing a plot

.pull-left[

``` r
x<-(0:100)/10
plot(x,x^3-13*x^2+39*x,
     type="l",
     xlab="time (hours)",
     ylab="temperature",
     cex.axis=1.5,cex.lab=1.5)
points(2,34,col="red",pch=16,
         cex=2)
```
]

.pull-right[
![](data:image/png;base64,#Figures/stepwise-plot2-1.png)
]
---
# Enhancing a plot

.pull-left[

``` r
x<-(0:100)/10
plot(x,x^3-13*x^2+39*x,
     type="l",
     xlab="time (hours)",
     ylab="temperature",
     cex.axis=1.5,cex.lab=1.5)
points(2,34,col="red",pch=16,
       cex=2)
*arrows(4,50,2.2,34.5)
```
]

.pull-right[
![](data:image/png;base64,#Figures/stepwise-plot3-1.png)
]
---
# Enhancing a plot

.pull-left[

.pull-right[
![](data:image/png;base64,#Figures/stepwise-plot4-1.png)
]

---
# Enhancing a plot

.pull-left[

``` r
x<-(0:100)/10
plot(x,x^3-13*x^2+39*x,
     type="l",
     xlab="time (hours)",
     ylab="temperature",
     cex.axis=1.5,cex.lab=1.5)
points(2,34,col="red",pch=16,
       cex=2)
arrows(4,50,2.2,34.5)
text(4.15,50,"local maximum",
     adj=0,col="blue",cex=1.5)
lines(x,30-50*sin(x/2),
      col="blue")
```
]

.pull-right[
![](data:image/png;base64,#Figures/stepwise-plot5-1.png)
]

---
# Enhancing a plot

.pull-left[

.pull-right[
![](data:image/png;base64,#Figures/stepwise-plot6-1.png)
]

---
# Graphical parameters (I)

You can change the default value of many graphical parameters via _par_ (see [?par](https://www.rdocumentation.org/packages/graphics/versions/3.5.1/topics/par)). For example to reset the background of a plot to
green:

``` r
> par("bg")
```

```
# [1] "white"
```

``` r
> par(bg="green")
> par("bg")
```

```
# [1] "green"
```

---
# Graphical parameters (II)
Any plot that you'll make from now on will have a green background:

``` r
> plot(x, x^3 - 13 * x^2 + 39 * x)
```

![](data:image/png;base64,#Figures/par3-1.svg)

---
# Graphical parameters (III)

But luckily you can switch back:

``` r
> par(bg="white")
> plot(x, x^3 - 13 * x^2 + 39 * x)
```

![](data:image/png;base64,#Figures/par4-1.svg)

---
# Graphical parameters: saving defaults

``` r
> par.defaults <- par(no.readonly=TRUE)
> par(bg="green")
> par(par.defaults)
> plot(x, x^3 - 13 * x^2 + 39 * x)
```

![](data:image/png;base64,#Figures/par5-1.svg)
---
# Graphical parameters (IV)

Other often used parameters/arguments:
- _lwd_ sets the line width
- _las_ to rotate axis symbols
- _mfrow_ and _mfcol_ enable multiple plots in one figure
- _mar_ to change the default margins of the figure

``` r
> plot(x,x^3-13*x^2+39*x,type="l",xlab= "time (hours)",
+      ylab="temperature",lwd=3,las=1,cex.axis=1.3,cex.lab=1.5)
```

![](data:image/png;base64,#Figures/par6-1.svg)

---
# Histogram

Use `hist` for plotting histograms. See [?hist](https://www.rdocumentation.org/packages/graphics/versions/3.5.1/topics/hist) for the many arguments of this function.

``` r
> hist(titanic3$age,breaks=15,freq=FALSE,cex.axis=1.5,cex.lab=1.5)
```

![](data:image/png;base64,#Figures/hist-1.png)

---
# Boxplot (I)

.pull-left[
The function `boxplot` can be used on a vector:

``` r
boxplot(titanic3$fare,
        ylim=c(0,300),
        ylab="fare", 
        cex.axis=1.5,
        cex.lab=1.5
        )
```
]
.pull-right[
![](data:image/png;base64,#Figures/boxplot1-1.png)
]

---
# Boxplot (II)

.pull-left[
Or using the formula interface (with ~):

``` r
boxplot(fare~pclass,
        data=titanic3,
        ylim=c(0,300),
        ylab="fare", 
        cex.axis=1.5,
        cex.lab=1.5
        )
```
With the formula interface you can also simply use `plot`.
]
.pull-right[
![](data:image/png;base64,#Figures/boxplot2-1.png)
]

---
# Interactive plots

``` r
> library(plotly)
> dat = data.frame(x=(0:100)/10,y=x^3-13*x^2+39*x)
> plot_ly(data=dat,x=~x,y=~y)
```

---
class: center, middle

# Thanks!

Slides created via the R package [**xaringan**](https://github.com/yihui/xaringan).