Building R Markdown reports without RStudio

January 11, 2022

RStudio is a powerful and user-friendly platform for developing and performing R based data analysis. Coupled with R Markdown, one can easily generate visually rich reports that are one of, if not the, most used feature by the R community at EMBL to communicate results.

When the popular GBCS RStudio server backed by the large seneca server is too busy, or if you need a convenient way to generate R Markdown reports in parallel or as part of elaborate pipelines, you can use the following script:

#!/usr/bin/env bash

if [ "2" -gt "$#" ]; then
  echo "Usage: $0 script.Rmd path/to/output.html arg1=\'value1\' arg2=\'value2\' ..."
  exit 1
fi

function commas() { local IFS=","; echo "$*"; }

FILE="$1"
shift
OUTNAME="$(basename "$1")"
OUTDIR="$(dirname "$1")"
shift

echo "Running: R -e \"rmarkdown::render('$FILE',output_format='html_document',output_dir='${OUTDIR}',output_file='${OUTNAME}',params=list($(commas "$@")))\""
R -e "rmarkdown::render('$FILE',output_format='html_document',output_dir='${OUTDIR}',output_file='${OUTNAME}',params=list($(commas "$@")))"

saving the above content on a file called Rmarkdown and adding it to your shell’s $PATH will allow you to execute

Rmarkdown my_analysis.Rmd output_folder/output.html arg1='value1' arg2='value2'

and build or knit R Markdown reports without RStudio.

To use the above command with the EMBL cluster, don’t forget to load the appropriate R module (e.g. module add R-bundle-Bioconductor-GBCS/3.11-foss-2020a-R-4.0.0) beforehand.

See also this approach from Francesco Tabaro to build a report by submitting a SLURM job directly from R.

If you see errors related to X11 display, try adding options(bitmapType='cairo') to your script or ~/.Rprofile, as described in the GBCS wiki.

Happy reporting!
Renato

Photo by Fotis Fotopoulos on Unsplash