remlapmot / mrdags

Code to draw DAG and SWIG figures for Mendelian randomization studies

mrdags

Code to draw directed acyclic graphs (DAGs), single world intervention graphs (SWIGs), and figures for Mendelian randomization (MR) analyses.

To build the output (index.html) open the project in RStudio (e.g., double-click mrdags.Rproj). Then open index.qmd and click the Render button or Render Website button in the Build pane. Or run in the R Console

quarto::quarto_render()

or after the packages or renv or R version has been updated

quarto::quarto_render(cache_refresh = TRUE)

Or run in your terminal

quarto render

or

quarto render --cache-refresh

Rendered at https://remlapmot.github.io/mrdags/

System requirements

Linux system requirements

The following dependencies for ggdag and I think igraph are required. Install them on Debian/Ubuntu with

sudo apt-get install glpk-utils libglpk-dev

Install the dependencies for pdftools with

sudo add-apt-repository -y ppa:cran/poppler
sudo apt-get update
sudo apt-get install -y libpoppler-cpp-dev

macOS system requirements

On macOS the LaTeX package dvisvgm requires the Ghostscript dynamically linked shared library libgs.dylib. Installing Ghostscript from Homebrew will provide this library.

brew install ghostscript

The path to libgs.dylib in the setup chunk in index.qmd should be general.

Also on macOS this project requires X11, which is easiest to obtain and install from https://www.xquartz.org/.

Additionally it is helpful to set the SHELL environment variable to the shell you use, e.g., Homebrew zsh by setting in your .Renviron file

SHELL=/opt/homebrew/bin/zsh

(Old note: If you have an Apple Silicon Mac you need to make sure you have Quarto version 1.2.56 or later because then the deno executable is arm64 and hence the arm64 libgs.dylib library from Homebrew will work.)

And on macOS you need to make sure the current user has write permission to /usr/local/bin by running the following command in Terminal, as per here.

sudo chown -R $(whoami) /usr/local/bin

Dependency packages

Using renv

This project uses renv, to install the required packages at the same versions that produced the rendered output, run in R

# install.packages("renv")
renv::restore()

Updating packages within renv

Run

renv::update()
renv::snapshot(prompt = FALSE)

Using devtools instead of renv

Alternatively, but without the guarantee that the package version numbers will be same that generated the output, run in R

# install.packages("devtools")
devtools::install_dev_deps()

This works because this repo includes a DESCRIPTION file.

TinyTeX

TinyTeX then needs to be installed with

tinytex::install_tinytex()

During a render, TinyTeX will install the LaTeX packages dvisvgm and pgf if they are missing.