Adding log-scaled tick marks to an axis with ggplot2 in R (CC325)
Pat recreates a figure published in mBio as a line plot with data using the geom_line and geom_errorbar functions from ggplot2 in R and composes them together using patchwork. Along the way he uses filter, summarize, geom_errorbar, geom_line, labs, scale_color_manual, scale_y_log10, guide_axis_logticks, coord_cartesian, and theme. The original paper is in an open access journal and can be found at https://journals.asm.org/doi/10.1128/mbio.01206-24. The newsletter describing how he would go about generating the figure can be found here.
Code
library(tidyverse)
library(ggtext)
library(glue)
library(patchwork)
set.seed(19760620)
fig2c_data <- tibble(
drug = rep(c("Gentamicin", "Ofloxacin", "Meropenem", "Colistin"), each = 36),
strain = rep(rep(c("PA01", "mutant", "mutant_arabinose"), each = 12),
times = 4),
rep = rep(1:3, times = 48),
time = rep(rep(c(0, 1, 2, 3), each = 3), times = 12)
) %>%
mutate(density = c(rnorm(3, mean = 5e6, sd = 2e6), #Gentamicin
rnorm(3, mean = 1e3, sd = 3e2),
rep(490, 6),
rnorm(12, mean = 5e6, sd = 2e6),
rnorm(3, mean = 5e6, sd = 2e6),
rnorm(3, mean = 1e3, sd = 5e2),
rep(490, 6),
rnorm(3, mean = 5e6, sd = 1e6), #Ofloxacin
rnorm(3, mean = 2e3, sd = 8e2),
rep(490, 6),
rnorm(12, mean = 5e6, sd = 2e6),
rnorm(3, mean = 5e6, sd = 1e6),
rep(490, 9),
rnorm(3, mean = 5e6, sd = 2e6), #Meromenem
rnorm(3, mean = 5e5, sd = 4e5),
rnorm(3, mean = 1e5, sd = 4e4),
rnorm(3, mean = 6e4, sd = 2e4),
rnorm(12, mean = 5e6, sd = 2e6),
rnorm(3, mean = 5e6, sd = 1e6),
rnorm(3, mean = 5e5, sd = 1e5),
rnorm(3, mean = 1e5, sd = 2e4),
rnorm(3, mean = 6e4, sd = 1e4),
rnorm(3, mean = 5e6, sd = 2e6), #Colistin
rnorm(3, mean = 5e3, sd = 3e3),
rnorm(3, mean = 1e3, sd = 4e2),
rnorm(3, mean = 8e2, sd = 3e2),
rnorm(3, mean = 6e6, sd = 2e6),
rnorm(3, mean = 6e3, sd = 3e3),
rnorm(3, mean = 2e3, sd = 3e2),
rnorm(3, mean = 1e3, sd = 3e2),
rnorm(3, mean = 5e6, sd = 2e6),
rnorm(3, mean = 5e3, sd = 3e3),
rnorm(3, mean = 1e3, sd = 4e2),
rnorm(3, mean = 8e2, sd = 3e2))
)
plot_drug_data <- function(drug_name){
fig2c_data %>%
filter(drug == drug_name) %>%
summarize(mean = mean(density),
sd = sd(density),
.by = c(strain, time)) %>%
ggplot(aes(x = time, y = mean, color = strain,
ymin = mean - sd, ymax = mean + sd)) +
geom_errorbar(color = "black", width = 0.2, linewidth = 1) +
geom_line(linewidth = 2) +
labs(x = "Time (h)",
y = "CFU/mL",
color = NULL,
title = drug_name) +
scale_color_manual(breaks = c("PA01", "mutant", "mutant_arabinose"),
values = c("black", "pink", "darkred"),
labels = c("PA01",
"Δ*iscU* P<sub>ara</sub>*iscU*",
"Δ*iscU* P<sub>ara</sub>*iscU* (+0.5% ARA)")) +
scale_y_log10(breaks = c(1e2, 1e3, 1e4, 1e5, 1e6),
labels = glue("10<sup>{2:6}</sup>"),
guide = guide_axis_logticks(
short = 1.5, mid = 1.5, long = 2.25)
) +
coord_cartesian(ylim = c(500, 1e7), expand = FALSE) +
theme_classic() +
theme(
legend.text = element_markdown(size = 18, margin = margin(l = 10, r = 30)),
legend.key.width = unit(40, "pt"),
axis.line = element_line(linewidth = 1),
axis.ticks = element_line(linewidth = 1),
axis.ticks.length.x = unit(5, "pt"),
axis.text.x = element_markdown(color = "black", size = 18,
margin = margin(t = 10)),
axis.title.x = element_text(size = 18,
margin = margin(t = 10)),
axis.text.y = element_markdown(color = "black", size = 18),
axis.title.y = element_text(size = 18),
panel.grid.major.y = element_line(color = "gray"),
plot.title = element_text(size = 18, hjust = 1, margin = margin(r = 20))
)
}
gentamicin <- plot_drug_data("Gentamicin") +
theme(plot.margin = margin(r = 40)
)
ofloxacin <- plot_drug_data("Ofloxacin")
meropenem <- plot_drug_data("Meropenem") +
theme(plot.margin = margin(r = 40, t = 20)
)
colistin <- plot_drug_data("Colistin") +
theme(plot.margin = margin(t = 20)
)
(gentamicin | ofloxacin) /
(meropenem | colistin) +
plot_layout(guides = "collect") &
theme(
legend.position = "bottom",
legend.margin = margin(t = 20, b = -8)
)
ggsave("iron_sulfur_resistance.png", width = 9.87, height = 8)