2024_kantnerova_et_al

Kantnerová et al. (2024) supplemental (🔗 GitHub repo)

This repository holds data and source code for Kantnerová, K, Kuhlbusch, N, Juchelka, D, Hilkert, A, Kopf, S, Neubauer, C. A guide to precise measurements of isotope abundance by ESI-Orbitrap MS. Nature Protocols, 2024. Some .raw files are not included here due to their size. These are available on MassIVE, records MSV000093222 and MSV000093223.

The rendered HTML reports of the notebooks can be viewed here:

What can I do with this code?

We hope that this code, or any part of it, might prove useful to other members of the scientific community interested in the subject matter. This repository is released under a Creative Commons BY (CC-BY) license, which means all code can be shared and adapted for any purpose as long as appropriate credit is given. See Attribution section for details. Most of the code is provided in R Markdown (see below).

What is R Markdown?

R Markdown is a so-called “literate programming” format that enables easy creation of dynamic documents with the open-source R language. HTML and PDF reports can be generated from R Markdown files using knitr and pandoc, which can be installed automatically with RStudio, and are fully integrated into this cross-platform IDE. All software used for these RMarkdown reports (R, RStudio, etc.) is freely available and completely open-source.

How can I run this code?

The quickest and easiest way is to use RStudio.

  1. Download and install R for your operating system
  2. Download and install RStudio for your operating system
  3. Download a zip file of this repository and unpack it in an easy to find directory on your computer
  4. Navigate to the directory and double-click the project.Rproj file to start RStudio and load this project.
  5. Install the required libraries by running the following command in the Console in RStudio: install.packages(c("rlang", "devtools", "tidyverse", "latex2exp", "cowplot", "readxl", "openxlsx", "isoorbi")) or by installing them manually in RStudio’s Packages manager. NOTE: the newest version of isoorbi is not on CRAN yet, install it with devtools::install_github("isoverse/isoorbi", ref = "dev-v1.3").
  6. Open the .qmd notebooks in the RStudio file browser (e.g. shot_noise.qmd)
  7. To render an HTML report, select File –> Render Document from the menu. The HTML report will be displayed upon successful completion and is saved as a standalone file in the same directory. All generated data figures are saved as PDF and PNG in the plots sub-directory. All generated data tables are saved as XLSX in the output sub-directory.

Troubleshooting notes

The R Markdown files in this repository make use of various R modules for data processing, plotting and modelling. All of these should be installed automatically when the first R Markdown file is knitted (if the knitting fails because of a missing package, please install it manually, an error will indicate which package could not be installed).