Twenty figure types that show up again and again in top-journal papers, rebuilt from scratch in R with ggplot2. Each one runs on simulated data, so the whole repository works on a fresh clone with nothing to download.
Every case is a small self-contained recipe: a simulate.R that generates the
data in base R, and a plot.R that builds and saves the figure. There are no
data files. The data is generated from a fixed seed each time, so a re-run gives
the same figure, and swapping in your own data is a matter of matching the
column names the simulator returns.
The figures mirror the structure of published examples (Manhattan and volcano plots, Circos diagrams, Sankey flows, raincloud and split-violin plots, treemaps, correlation and Mantel heatmaps, and more). All data here is simulated; none of it is real or downloaded.
# 1. install the packages (once)
Rscript setup.R
# 2. render everything
Rscript scripts/run_all.R
# or render a single case
Rscript -e 'source("cases/04-manhattan-twas/plot.R")'Run the scripts from the repository root. Paths are relative, so plot.R finds
R/theme_case.R and its own simulate.R without any setup.
scripts/run_all.R runs each case in its own R process and prints a pass/fail
table, so a broken simulator or plot shows up immediately.
| # | Figure type | Based on a figure from |
|---|---|---|
| 01 | Individualized error dot-plot | Nature Microbiology |
| 02 | Grouped error dot-plot | Nature Cell Biology |
| 03 | Multi-group volcano | Nature Communications |
| 04 | Manhattan (TWAS) | iMeta |
| 05 | Paired boxplot | Nature Microbiology |
| 06 | Raincloud | Nature Communications |
| 07 | Swimmer plot | Nature |
| 08 | Importance bars + abundance streams | Nature Communications |
| 09 | Grouped variance bars with letters | Int. J. Mol. Sci. |
| 10 | Circos fusion-gene | Nature Communications |
| 11 | Module interaction network | Nature Communications |
| 12 | Sankey with an enrichment bubble panel | Nature Communications |
| 13 | Discrete (binned) heatmap | Nature Microbiology |
| 14 | Mantel composite heatmap | Nature Microbiology |
| 15 | Multi-group correlation heatmap | Nature Communications |
| 16 | Polar-coordinate heatmap | Nature Communications |
| 17 | Multi-level Sankey | Nature Communications |
| 18 | Treemap | Nature Communications |
| 19 | Mosaic and sunburst | Nature Communications |
| 20 | Split violin | Nature Communications |
ggplot2-20-journal-cases/
├── README.md
├── setup.R # install every required package
├── R/theme_case.R # shared theme, palettes, saver
├── scripts/run_all.R # render every case, one process each
└── cases/
├── 01-error-dotplot/ # simulate.R, plot.R, figures/
├── ...
└── 20-split-violin/
Core: ggplot2, dplyr, tidyr, ggrepel, patchwork. By case: ggalluvial (Sankey),
treemapify (treemap), circlize (Circos), gghalves (raincloud and split violin),
ggh4x (per-panel strips), igraph and ggraph (network). setup.R installs all of
them, including the archived build of gghalves.
MIT. The code is original and the figures are independent rebuilds from simulated data.