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Reproducible R Projects with WorkflowR

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Nhi Hin edited this page Mar 25, 2021 · 3 revisions

Step 0 - Initialisation (optional - for increased reproducibility)

NOTE: I highly recommend skipping this step for most projects nowadays as re-installing everything takes ages. Will use for projects where there is an important need to have everything be 100% reproducible.

  • Create a new project as normal in RStudio (without git initialisation, as WorkflowR will create one later).
  • Before writing any code, load the Packrat R package library(packrat) and initialise Packrat using packrat::init("~/pathTo/PROJECTNAME"). Packrat is a library manager for R and RStudio that isolates the packages used to a particular project. This ensures that the exact packages and their versions that were used in a particular project can be carried in a modular way with the project, making it easy to reproduce. More information about Packrat can be found in their documentation.
  • After installing new packages with Packrat (using install_packages()), use packrat::snapshot() to save the changes.

Step 1 - Setting up WorkflowR

We will use WorkflowR to manage and organise the directories and files for the project.

  1. Install workflowR and load the package using library(workflowr).
  2. Run the following in the Console to set up WorkflowR:
wflow_start("~/pathTo/PROJECTNAME", existing = TRUE, overwrite = TRUE)
  1. Run wflow_build() in the Console.
  2. Build and commit the website using wflow_publish().

Note: The status of files can be checked using wflow_status().

  1. To deploy the website, run the following in Console: wflow_use_github("nhihin") (replace with GitHub username) and select option 1 to automatically create the repository. NOTE: When you have to enter your password for this step, instead of your GitHub password, create a Personal Access Token here and enter the value of that token instead! This is because GitHub is deprecating the use of passwords directly by 3rd party programs (including RStudio), see here.
  2. The Git tab on RStudio can now be used as normal to commit, push, and pull files. If it isn't showing up, usually restarting RStudio fixes this.

Note: If the GitHub repository needs to be private (e.g. sensitive/client data), this needs to be changed immediately after step 5 on the GitHub website, see here.

Making a new analysis file

  • Use wflow_open("analysis/your-file-name.Rmd") to make a new analysis RMarkdown.
  • Files must be committed using wflow_build("analysis/your-file-name.Rmd") and pushed using wflow_publish("analysis/your-file-name.Rmd").
  • Globbing is useful for committing and pushing, for example, wflow_build("analysis/*.Rmd") will build all .Rmd files in the analysis directory.

Editing the navigation bar

  • This is important to do early on, as the navigation bar defined will be used across every analysis file created. This saves time if defined early on.
  1. Open the file in analysis/_site.yml.
  2. Under left: is where you can define links in the navigation bar. Text is the name of the link while href is the URL of the link. This is a relative url pointing to the analysis directory so no need to put in the full path.
  3. Typically one link for one analysis file for each specific step of the analysis. The menu: thing is used to define a drop-down menu, which is helpful for organising many analysis pages which are related to each other.

Example:

name: Project Name
output_dir: ../docs
navbar:
  title: Project Name
  left:
  - text: Home
    href: index.html
  - text: About
    href: about.html
  - text: Setup
    href: setup.html
    menu:
      - text: "Pre-processing"
      - text: "cellranger pipeline"
        href: cellranger.html
      - text: "Initial analysis"
      - text: "Merge datasets with Seurat"
        href: import-data.html
      - text: "Aggregate with cellranger"
        href: import-merged-data.html
  - text: License
    href: license.html
  right:
  - icon: fa-github
    text: Source code
    href: https://github.com/nhihin/Heart-scRNAseq
output:
  workflowr::wflow_html:
    toc: yes
    toc_float: yes
    theme: cosmo
    highlight: textmate

Publishing the website on GitHub pages

  • Once all RMarkdown files have been published as .html files (and pushed to GitHub using wflow_publish), go to Settings > GitHub Pages and choose “master branch docs/ folder” as the Source. See screenshot below.

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