Plot dissociation kinetics in ggplot2

Introduction

During the past weeks I was running a lot of antibody kinetics experiments on the Biacore T200 instrument. Unfortunately, the Biacore evaluation software is an older version and cannot be used to make publication quality plots. As a result, I thought of using ggplot2 to plot biacore kinetics data. Lets jump right in.

Preparing the data

Load required libraries:

library(readr)
library(tidyr)
library(dplyr)
library(ggplot2)

Import the data into R Studio:

raw_data <- read_delim(
  "biacore_kinetics.txt", 
  escape_double = FALSE, 
  trim_ws = TRUE
)

Preparing the data for plotting:

# The first column (1) is time in seconds
# The RU (response units) are stored in variables ending with _Y.
data_final <- raw_data |> select(c(1, ends_with("Y")))

# Column renaming (time, F = fitted values, R = raw values)
names(data_final) <- c("time", "2 nM-R", "2 nM-F", "4 nM-R", "4 nM-F", "8 nM-R", 
                       "8 nM-F", "16 nM-R", "16 nM-F", "32 nM-R", "32 nM-F", 
                       "8 nM (rep 2)-R", "8 nM (rep 2)-F")

# Transformation of raw data to tidy data
# Separating the concentrations from raw or fitted data
# Filtering out the duplicate 8nM samples
plot_data <- data_final |> 
  pivot_longer(!time, names_to = "sample", values_to = "values") |>
  separate(col=sample, into=c("conc", "type"), sep='-') |> 
  filter(conc != "8nM (rep 2)")

# Seperating raw and fitted RU
raw <- plot_data |> filter(type == "R")
fitted <- plot_data |> filter(type == "F")

The final plot

ggplot(NULL) +
  geom_line(
    data = raw,
    aes(x = time, y = values, group = conc)
  ) +
  geom_line(
    data = fitted,
    aes(x = time, y = values, group = conc),
    color = "red"
  ) +
  scale_x_continuous(
    expand = c(0, 0), 
    limits = c(NA, 600),
    n.breaks = 14, 
    labels = scales::label_number(suffix = "s")
  ) +
  scale_y_continuous(
    expand = c(0, 0),
    limits = c(-2, 15)
  ) +
  theme_linedraw(base_size = 20) +
  labs(
    caption = "Note: Red line is fitted data",
    color = "Soluble CD16",
    x = "Time (seconds)",
    y = "Response units (RU)"
  ) +
  theme(
    legend.position = "none",
    axis.title.x  = element_text(size = 13, face = "bold"),
    axis.title.y  = element_text(size = 13, face = "bold"),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank()
  )