Raukr 2023 • Course materials

NBIS Summer School • Advanced R for Bioinformatics

Requirements

To edit, preview and render documents, you need one or more of the following requirements:

• You must use Quarto>=1.2.269
• If using RStudio, use v2022.07.1 or newer
• VSCode is a good alternative to RStudio for quarto documents
• You need to install the R packages necessary for your topic/document

‼️ Be wary of using the visual editor! It may mess up the code formatting.

Adding/Modifying topics

• Fork the repository and clone locally

• Keep the topic name simple, preferably one word

• To add a topic, create

  • slides/topic/index.qmd

  • labs/topic/index.qmd

  • The YAML metadata should minimally look like this:

    ---
    title: "Topic"
    author: "Author"
    description: "This topic covers this and that."
    format: html
    ---
    

• format must be html for reports and revealjs for presentations

• For assets relating to the document (figures, files etc), create an assets folder

  • slides/topic/assets/
  • labs/topic/assets/

💡 The document can be live previewed to view changes. Preview is automatically updated on saving the document. Sometimes, the preview can look a bit wonky, in which case, cancel and rerun.

• To preview, run in terminal
  • quarto preview slides/topic/index.qmd
  • quarto preview labs/topic/index.qmd
  • Saving the file updates the preview

💡 The document is rendered to the specified output format in the output directory.

• To render, run in terminal
  • quarto render slides/topic/index.qmd
  • quarto render labs/topic/index.qmd
  • Rendered files are written to /docs
  • To view in browser, open
    • docs/slides/topic/index.html
    • docs/labs/topic/index.html

‼️ Do not run quarto render as it will remove everything from docs/ and attempt to render all the files. This might overwrite someone else's materials and also break since you won't have their R packages installed. So, only render your files.

• Finally commit changes (both source files and rendered files)

git stage .
git commit -m "Added topic"

• Push changes to your fork and send a pull request

Tips & Conventions

• For compute heavy steps, save intermediates and read them in

• Be mindful of the size of files

  • Store large data files elsewhere (dropbox, google drive etc) and link them
  • If you have images that are more than a few hundred KB in size, scale them down to about 600px-800px and compress them

• Use simple topic labels and do not make them needlessly complex

• The qmd files must be in the correct location when rendering/previewing else metadata from config is not used.

• Declare R packages at the beginning of every qmd document

• qmd files must have a format defined, either format: html or format: revealjs

• Make a note of the default execute settings in _quarto.yml. This applies to all documents. You can override this by copying the code below to the yaml part of your document and modifying it.

  execute:
    eval: true
    echo: false
  

• Use level 2 heading (##) as the highest level heading

• Bullet points are defined by -

• Define options in code chunks using #| like #| echo: true

• Adjusting dimension of images ![Caption](path/to/image.jpg){width="50%"}

• Divs are defined using ::: and classes are defined using {.class}

  • Example of a class on a div

  ::: {.callout-note}
  content
  :::
  

• Example of a class on a span [Content]{.class}

• Columns are defined as such

:::: {.columns}
::: {.column width="50%"}
Contents
:::
::: {.column width="50%"}
Contents
:::
::::

• Remember to spell-check your document

  • Language used is en-us

• To view a demo report, click here

RevealJS

These are slide specific info. Comparisons here are to xaringan used previously for RaukR.

• Slides are defined by ## rather than ---
• Manual increment is defined by . . . rather than --
• Horizontal rule is defined by --- rather than ***
• Presenter notes are defined by :::{.notes} content ::: rather than ???
• For small notes in the bottom of the slide, you can use

::: {.aside}
Contents
:::

• If content overflows the slide in vertical direction, add class .scrollable

::: scrollable
content
:::

• To view a demo presentation, click here