Welcome to ggplot2

EE BIOL C177/C234

Chuliang Song

Today’s Menu 🎯

1. Why focus on graphs?
2. The grammar of graphics concept
3. Build scatter plots with ggplot2
4. Customize with aesthetics & themes

Why Graphs?

Visuals Are Powerful

• Humans are visual beings
• Most readers will skim your paper
• A well-designed graph makes your key findings clear
• ggplot2 provides a structured approach to visualization
• Massive ecosystem of extension libraries

Your First ggplot2 Graph

History of Grammar of Graphics

• Conceived by statistician Leland Wilkinson
• Breaks graphics down into fundamental components
• Laid the mathematical foundation for ggplot2
• Widely adopted across data science

Our First Scatter Plot

library(ggplot2)
library(palmerpenguins)
ggplot(
  data = penguins,
  aes(x = bill_length_mm, y = bill_depth_mm)
) +
  geom_point()

Dissecting the Code

library(ggplot2)
library(palmerpenguins)
ggplot(
  data = penguins,
  aes(x = bill_length_mm,
      y = bill_depth_mm)
) +
  geom_point()

• ggplot() — start a new plot
• data = penguins — specify the dataset
• aes() — map variables to axes
• + — add layers (like Photoshop!)
• geom_point() — draw points

The Grammar of Graphics

Every plot has the same grammar:

ggplot(
  data = <DATA>,
  aes(x = <X>, y = <Y>)
) +
  <GEOM_FUNCTION>()

Data → Aesthetics → Geometry = a plot!

Tuning Our Plot

Adding Color by Species

ggplot(
  data = penguins,
  aes(
    x = bill_length_mm,
    y = bill_depth_mm
  )) +
  geom_point(aes(color = species))

Adding Shape Too

ggplot(
  data = penguins,
  aes(
    x = bill_length_mm,
    y = bill_depth_mm
  )) +
  geom_point(aes(color = species, shape = species))

Themes

Don’t Use the Default Theme!

The grey background wastes ink and looks bland. Use theme_bw():

ggplot(
  data = penguins,
  aes(x = bill_length_mm, y = bill_depth_mm)
) +
  geom_point(aes(color = species, shape = species)) +
  theme_bw()

Explore Other Themes

Try theme_minimal(), theme_classic(), or packages like jtools:

ggplot(
  data = penguins,
  aes(x = bill_length_mm, y = bill_depth_mm)
) +
  geom_point(aes(color = species, shape = species)) +
  jtools::theme_nice()

Exercise

Plot body_mass_g vs bill_depth_mm, colored by species:

Summary

• ggplot2 uses the grammar of graphics
• Data → Aesthetics → Geometry
• Map variables to color, shape, size, etc.
• Always change the default theme!