Customizing axes in a 1D scatter plot using the ggplot2 package in R (CC305)

October 14, 2024 • PD Schloss • 1 min read • •

Pat recreates a scatter plot that has a missing x-axis using the geom_point function from ggplot2 in R using geom_point. He customizes the appearance to match the original figure using the geom_vline, geom_hline, scale_color_manual, scale_x_continuous, scale_y_continuous, labs and theme functions. The plot is is Figure 1A from the paper, “Exploring novel microbial metabolites and drugs for inhibiting Clostridioides difficile” by Ahmed Abouelkhair and Mohamed Seleem (https://journals.asm.org/doi/10.1128/msphere.00273-24). The newsletter describing how I would go about generating the figure can be found at https://shop.riffomonas.org/posts/building-data-visualization-intuition.

Code

library(tidyverse)
set.seed(19760620)

sim_data <- tibble(
  compound = 1:527,
  percent_inhibition = sample(
    c(rnorm(n = 464, mean = 0, sd = 30),
      runif(63, 91, 100))
    )
  ) %>%
  mutate(strong = percent_inhibition >= 90)

sim_data %>%
  ggplot(aes(x = compound, y = percent_inhibition, color = strong)) +
  geom_vline(xintercept = 1, linewidth = 1) +
  geom_hline(yintercept = c(0, 90),
             linetype = c("solid", "dashed"),
             linewidth = c(1, 0.5)) +
  geom_point(show.legend = FALSE) +
  scale_color_manual(
    breaks = c(FALSE, TRUE),
    values = c("seagreen", "maroon") # "gold4" was actual greenish color
  ) +
  coord_cartesian(clip = "off") +
  scale_x_continuous(expand = c(0,0)) +
  scale_y_continuous(limits = c(-101, 101),
                     breaks = seq(-100, 100, by = 50),
                     expand = c(0,0)) +
  labs(x = NULL,
       y = "Inhibition of Bacterial Growth %") +
  theme_classic() +
  theme(
    axis.line.x = element_blank(),
    axis.ticks.x = element_blank(),
    axis.text.x = element_blank(),
    axis.line.y = element_blank(),
    axis.ticks.y = element_line(linewidth = 1),
    axis.ticks.length.y = unit(5, "pt"),
    axis.text.y = element_text(face = "bold"),
    axis.title.y = element_text(face = "bold")
  )