Plotting and data visualization in base R Answer Key

Author

Will Gammerdinger

Published

December 5, 2025

Exercise 1

Change the color scheme in the scatterplot, such that it reflects the genotype of samples rather than celltype.

# Create factor of genotype
new_metadata$genotype <- factor(new_metadata$genotype)

# Create plot
plot(samplemeans ~ age_in_days, data=new_metadata,
     main="Expression changes with age",
     xlab="Age (days)",
     ylab="Mean expression",
     pch="*",
     cex=2.0,
     col=c("blue", "green")[genotype])

# Add legend
legend("topleft",
       pch="*",
       col=c("blue", "green"),
       c("A", "B"),
       cex=0.8,
       title="Genotype")

Use R help to find out how to increase the size of the text on the axis labels.

# Open graphical parameters help page
?par

---
title: "Plotting and data visualization in base R Answer Key"
author:
  - Will Gammerdinger
date: "2025-12-05"
---

```{r}
#| label: load_data_libraries
#| echo: false
# Load the purrr package
library(purrr)

# Load data
metadata <- read.csv(file="data/mouse_exp_design.csv")
rpkm_ordered  <- read.csv("data/ordered_counts_rpkm.csv",
                          header=T, row.names = 1)

samplemeans <- map_dbl(rpkm_ordered, mean) 

age_in_days <- c(40, 32, 38, 35, 41, 32, 34, 26, 28, 28, 30, 32)        
new_metadata <- data.frame(metadata, samplemeans, age_in_days) 
```

# Exercise 1

1. Change the color scheme in the scatterplot, such that it reflects the `genotype` of samples rather than `celltype`.

```{r}
#| label: color_by_genotype
# Create factor of genotype
new_metadata$genotype <- factor(new_metadata$genotype)

# Create plot
plot(samplemeans ~ age_in_days, data=new_metadata,
     main="Expression changes with age",
     xlab="Age (days)",
     ylab="Mean expression",
     pch="*",
     cex=2.0,
     col=c("blue", "green")[genotype])

# Add legend
legend("topleft",
       pch="*",
       col=c("blue", "green"),
       c("A", "B"),
       cex=0.8,
       title="Genotype")
```

2. Use R help to find out how to increase the size of the text on the axis labels.

```{r}
#| label: par_help
#| eval: false
# Open graphical parameters help page
?par
```