ggchemplot: an R package for publication-quality 2D chemical structures

Sat, 09 May 2026 00:37:00 +0000

This week I faced a situation that many biochemists should relate: preparing figures for a paper in which you have to draw chemical structures. The commercial software ChemDraw, initially developed in 1985 (Evans, 2014), still is the gold standard for drawing publication-quality 2D chemical structures. Because the signature is expensive and the free software available did not met my needs, I started to look for alternatives in R, specially as a ggplot2 (Wickham, 2016) extension. I reasoned that such a fundamental kind of visualization in (bio)chemical and medical sciences would count with a nice R package. There was none.

My next move was to load as a dataframe in R a Structure Data File (SDF) of a 2D chemical compound downloaded from PubChem. The file specify atoms and coordinates. That’s all we need for ggplot2. After the initial plot, I realized that I could make something out of it. After four days writing functions and packaging them, today I used it for creating a figure for my manuscript. Here, I will show how my first ggplot2 extension might help you, R user.

The `ggchemplot` R package

The workflow of ggchemplot follows three steps:

Parse a SDF file with ggchemplot1().
Visualize the preliminary plot and modify the data with helper functions for polishing.
Plot the final visualization with ggchemplot2().

Short tutorial

Install the package from my GitHub repository.

# Install the remotes package if not already installed
install.packages("remotes")

# Install ggchemplot from GitHub
remotes::install_github("JPFQueiroz/ggchemplot")

The input file in this example (P1_pyridone.sdf) was prepared through the drawing tool of PubChem. Other R users might also prepare the input structure directly from R with rcdk (Guha, 2007). Use ggchemplot1 to parse the file and generate the initial data object.


# Load ggchemplot
library(ggchemplot)

# Parse the data and generate initial plot
p1 <- ggchemplot1(sdf_file = "P1_pyridone.sdf")

# Check the initial plot
p1$plot

Quickly visualize the atom and bond ids in p1$atoms on the plot with the argument show_ids = TRUE in ggchemplot2(). The ids visualization can guide through the polishing step, where many functions use as argument ids of atoms or bonds.


# Load dplyr to use the pipe operator %>% 
library(dplyr)

p1 %>% 
  ggchemplot2(show_ids = TRUE)

Polish the visualization using the arguments available in ggchemplot1(), modifying the underlying data with helper functions or through manual wrangling of the dataframe objects, and finally to ggchemplot2().


# Publication-quality plot
p1 <- ggchemplot1(
  sdf_file = "P1_pyridone.sdf",
  title = NULL,
  collapse_hydrogens = TRUE,
  rotation = 90,
  label_padding = 1,
  show_atom_circles = TRUE,
  hide_carbon_circles = TRUE,
  circle_stroke = 0,
  show_atom_labels = TRUE,
  hide_carbon_labels = TRUE,
  bond_width = 2,
  atom_size = 18,
  label_size = 12,
  double_bond_offset = 0.3,
  custom_atom_colors = NULL,
  paint_it_black = TRUE,
  H_offset = c(0.50, 1)) %>% 
  change_label(atom_id = 7, new_label = "Fe") %>% 
  add_hashed_bond(from_id = 7, to_id = 11, 
                  wedge_thickness = 0.3,n_hashes = 6,
                  shorten = c(0.3, 0)) %>% 
  ggchemplot2()

# Plot
p1

The basic tutorial ends here. You can cite ggchemplot (Fernandes-Queiroz, 2026) in your publications using the BibTex citation below. Your feedback is welcome.

@software{ggchemplot,
  author       = {João Pedro Fernandes Queiroz},
  title        = {JPFQueiroz/ggchemplot: ggchemplot: an R package for visualization of chemical structures},
  month        = may,
  year         = 2026,
  publisher    = {Zenodo},
  version      = {v0.2-beta.1},
  doi          = {10.5281/zenodo.20088880},
  url          = {https://doi.org/10.5281/zenodo.20088880},
}

References

Evans, D. A. (2014). History of the harvard ChemDraw project. Angewandte Chemie International Edition, 53(42), 11140–11145.

Fernandes-Queiroz, J. P. (2026). JPFQueiroz/ggchemplot: Ggchemplot: An r package for visualization of chemical structures (Version v0.2-beta.1) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.20088880

Guha, R. (2007). Chemical informatics functionality in r. Journal of Statistical Software, 18(6).

Wickham, H. (2016). ggplot2: Elegant graphics for data analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org

ggplot2 | The Evolutionary Biochemist

ggchemplot: an R package for publication-quality 2D chemical structures

The ggchemplot R package

Short tutorial

References

The `ggchemplot` R package