Box plots in R

Required prerequisite(s)

You must have R installed on your computer and ideally also RStudio. See https://rstudio-education.github.io/hopr/starting.html for a guide.

It is recommended that you have followed the Concepts in Computer Programming and Introduction to R tutorials before starting.
An understanding of tidy data. See https://www.youtube.com/watch?v=KW1laBLEiw0
An understanding of the melt format in R: https://www.statology.org/melt-in-r/

This demonstration uses UnpairedDataset1.tsv as box plots are not always suitable for paired data.

Open RStudio
Read in the UnpairedDataset1.tsv file. The read.delim will automatically assign row 1 as a header so no extra flags need to be passed to it
```
unpaired <- read.delim(“UnpairedDataset1.tsv")
```
The package ggplots2 is best for creating figures. Install the package (if needed) and load the library
```
install.packages("ggplot2")
library(ggplot2)
```
To create a chart the data must in a ‘melted’ long format. Install the reshape 2 package (if needed) and then load the library
```
install.packages("reshape2")
library("reshape2")
```
Melt the data frame so it is in the right format for ggplot2
```
meltedUnpaired=melt(unpaired)
```
The steps below are different ways to create boxplots, we more options added at each step. You don’t have to run each in order this way, you can skip to step 9 for the full chart; steps 7 and 8 are just for illustrative purposes
We create the chart by telling ggplot2 we want the variable (groups) on the x-axis and the measurements (values) on the y-axis. It will calculate the summary statistics needed by istelf
```
ggplot(data=meltedUnpaired, aes(x=variable, y=value)) +geom_boxplot()
```

We can also add labels to each axis to better describe the data

ggplot(data=meltedUnpaired, aes(x=variable, y=value)) +geom_boxplot() +labs(y= "Measurement", x = "Group") 

We can also add colour each box by the group name and colour outliers in red

ggplot(data=meltedUnpaired, aes(x=variable, y=value, fill=variable)) +geom_boxplot(outlier.colour="red")+labs(y= "Measurement", x = "Group") 

Once happy with the chart, we can save it to file

ggsave(file="unpairedBoxplot.png", plot=last_plot())