Quarto - Setting up a "book" as a single notebook post?

[kubu4]

I want to have an R Project rendered as a single blog post, but the issue is that we generally organize our R Projects in the following fashion:

├── ceabigr.Rproj
├── code
│   ├── 02-te-all.sh
│   ├── 07-TE-intersect-meth.Rmd
│   ├── 10-TEm-TEcn.Rmd
│   ├── 11.1-haplotype.sh
│   ├── 11.2-haplotype.sh
│   ├── 11-RNAseq-snps.Rmd
│   ├── 12-lncRNA.Rmd
│   ├── 13-lncRNA-kallisto.Rmd
│   ├── 14-RNA-kallisto.Rmd
│   ├── 15-RNAseq.Rmd
│   ├── 16-DML-annotation.Rmd
│   ├── 17-Swiss-Prot-Annotation.Rmd
├── output
│   ├── 02-te-all
│   ├── 11-RNAseq-snps
│   ├── 12-lncRNA
│   ├── 13-lncRNA-kallisto
│   ├── 14-RNA-kallisto
│   ├── 15-Gene-expression-analysis
│   ├── 16-DML-annotation
│   ├── 17-Swiss-Prot-Annotation

Each Rmd file has a corresponding output directory of the same name.

So, if I followed this format (which I'd like to do), I'd have a .qmd file (instead of .Rmd file) for each type of analysis I'd run.

In the current usage of Quarto for our notebooks, each .qmd file would get rendered as separate notebook posts.

However, I'd like a single notebook post, but with the ability to go through all the analyses performed in the R Project.

I think the solution is to set up the R Project as a Quarto Book. This allows defining "chapters" and the resulting rendered HTML files show a table of contents across the multiple .qmd files.

Unfortunately, it seems like when the Quarto Book is rendered in the notebook, each individual .qmd file gets rendered as it's own notebook entry.

Anyone have any thoughts on how to get a Quarto Book to function as a single notebook entry?

[sr320]

Compiling multiple R Markdown or Quarto documents into a single notebook entry or blog post while retaining a structured and organized file system can be a bit tricky, but it's definitely doable with some workarounds. Here are some suggestions you might find helpful:

1. Single Master Document:
   • You can create a single master .Rmd or .qmd file that serves as a wrapper around all your individual analysis documents.
   • You can use the child option in the YAML header to include the content of the other R Markdown files.
   • Example:

        ```yaml
        ---
        title: "Master Document"
        output: html_document
        ---

        ```{r child='code/07-TE-intersect-meth.Rmd'}
        ```

        ```{r child='code/10-TEm-TEcn.Rmd'}
        ```
        ```

This way, when you knit the master document, all the child documents get rendered into a single HTML document.

2. Bookdown:

   • You can use bookdown instead of Quarto, which is designed to handle multi-document projects and can compile them into a single output.
   • Create an _bookdown.yml file to specify the order of the documents.
   • Example:

     rmd_files:
       - code/07-TE-intersect-meth.Rmd
       - code/10-TEm-TEcn.Rmd
       ...

   • Then, render the book with bookdown::render_book() to get a single HTML file with a table of contents.

3. Custom Script:

   • Write a custom script that programmatically concatenates your .qmd or .Rmd files into a single document before rendering.
   • This can be done with basic file I/O operations in R or another scripting language.

4. External Tools:

   • There are also external tools and platforms like Distill for R, which might provide more seamless integration for combining multiple R analyses into a single blog post or notebook entry.

5. Custom CSS/JS:

   • If the issue is more about the aesthetics or navigation, you might be able to solve the problem with custom CSS or JavaScript to create a single-page feel, or a navigable table of contents across multiple HTML documents.

6. Quarto Book:

   • Explore further the Quarto documentation or reach out to the Quarto community for support. There might be undocumented or advanced features that can address this specific use case.

7. Explore Other Tools:

   • If none of the above solutions work, you might want to explore other documentation or blog rendering tools that better fit your project structure and rendering needs.

[kubu4]

Interesting. Option 1 seems like the most straightforward way. I'll test it out and report back. Thanks!

When I asked ChatGPT, it didn't provide me with all of these options...