forestplotR

Journal-ready forest plots with uniform spacing, embedded fonts, and automated sizing for Mendelian-randomization (or any β/CI) results.

forestplotR turns a tidy CSV of β estimates and confidence intervals into publication-quality SVG forest plots—every figure sized to the journal column width you choose, every font embedded for true vector fidelity. Built around ggplot2, ggpubr, and svglite, the script auto-iterates over outcomes (or exposures), applies crisp, uniform spacing, and saves each plot to a dedicated folder. Ready for Cell, Nature, or your next bioRxiv pre-print.

Uniform spacing, automatic sizing, zero Illustrator fuss.

---

Why use this script?

• Plug-and-plot – drop in a tidy CSV of β / CI values and run.
• True vector output – fonts embedded in‐file via showtext + svglite.
• Auto-sizing – choose a single (88 mm) or double (180 mm) column; row height scales automatically.
• Batch mode – one SVG per outcome (or exposure) written to figs_highimpact/.
• Journal aesthetics – built on theme_pubr(), dashed zero line, consolidated legend.

---

🗂 Input format

column	example value	notes
exposure	Serine	becomes y-axis label
outcome	Type 2 Diabetes	used to split output files (SPLIT_VAR)
method	IVW	plotted as colour / shape
beta	-0.17	point estimate
ci_lower	-0.24	95 % CI lower bound
ci_upper	-0.10	95 % CI upper bound
(alt.) SE	0.037	script converts SE → CI if CI columns absent

Save as your_results.csv (or change CSV parameter).

---

Quick start

# clone
git clone https://github.com/SidSin0809/forestplotR.git
cd forestplotR

# recruitment.txt (dependencies & environment)
install.packages(c(
  "tidyverse","ggpubr","patchwork",
  "svglite","showtext","RColorBrewer"
))

# run
Rscript forestplotR.r \
    --csv         your_results.csv \
    --split_var    outcome \
    --col_width    single \
    --out_dir      figs_highimpact

Customising

Column width – switch COL_WIDTH to "double" for 180 mm figures.

Facet wrap – default is facet_wrap(~ outcome, ncol = 5); edit for columns / label wrapping.

Colours & shapes – palette is RColorBrewer::Dark2; adjust in make_forest().

Row height – tweak row_h_mm in opt_dims() if labels overlap.

Citation

If this script accelerates your manuscript, a citation or acknowledgment is appreciated