[Bioc-devel] improving navigation within workflows

[Aaron Lun]

Hi Andrzej,

Interesting. I also didn't realize that we could get figure referencing 
via bookdown, that's nice to know. I was thinking that the floating TOC 
could go onto the right margin, but I guess that doesn't fit anymore now 
that you have the footnotes and figure captions.

CRAN-style links might be the best compromise, e.g., if they can be 
placed in the right margin. A simple set of three links 
(<previous><contents><next>) beside each section/subsection heading 
would probably sufficient for effective navigation, without using up too 
much space.

Cheers,

Aaron

On 17/07/17 00:35, Andrzej Oleś wrote:
> Hi Aaron,
> 
> thanks for your feedback. We are currently looking into ways of 
> improving the building of workflows for the website in order to enable 
> cross references, html widgets, and similar. So far these were not 
> supported because of some technical constraints of the current 
> implementation which involves rendering the workflows into an 
> intermediate .md file. The new approach will overcome these limitations 
> by skipping this intermediate step and rendering directly to html. For a 
> preview see: 
> https://www.bioconductor.org/help/workflows/testproj/testfile/ (it also 
> uses a slightly modified layout with some of the supporting information 
> such as figure and table captions, or footnotes moved to the right column)
> 
> Regarding the navigation, a floating TOC would be in principle possible 
> in the new implementation. It is not entirely clear to me, however, 
> weather this will visually work with the bioconductor.org 
> <http://bioconductor.org> website template. Links to the TOC, such as 
> ones in e.g. 
> https://www.bioconductor.org/help/workflows/highthroughputassays could 
> be relatively easily inserted automatically after each section. Static 
> CRAN-like solution as you mentioned it would probably require some more 
> work.
> 
> Cheers,
> Andrzej
> 
> On Sun, Jul 16, 2017 at 9:36 PM, Aaron Lun <alun at wehi.edu.au 
> <mailto:alun at wehi.edu.au>> wrote:
> 
>     Indeed, that's exactly what I was thinking of. I have a floating TOC in
>     my own Rmarkdown files, but I'm not sure if it's supported by the
>     workflow builder, given that it adds a separate hyperlinked TOC to the
>     start of the workflow page.
> 
>     On 16/07/17 19:29, Vincent Carey wrote:
>     > like this?
>     >
>     > http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html
>     <http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html>
>     >
>     > On Sun, Jul 16, 2017 at 11:53 AM, Aaron Lun <alun at wehi.edu.au <mailto:alun at wehi.edu.au>
>     > <mailto:alun at wehi.edu.au <mailto:alun at wehi.edu.au>>> wrote:
>     >
>     >     Hello all,
>     >
>     >     I was wondering if there's any plans to improve the navigation for the
>     >     BioC workflows. I was looking at my simpleSingleCell workflow:
>     >
>     >     https://www.bioconductor.org/help/workflows/simpleSingleCell/
>     <https://www.bioconductor.org/help/workflows/simpleSingleCell/>
>     >     <https://www.bioconductor.org/help/workflows/simpleSingleCell/
>     <https://www.bioconductor.org/help/workflows/simpleSingleCell/>>
>     >
>     >     ... and I've realized that it's gotten pretty long. It's a pain to keep
>     >     on scrolling up and down when I'm stuck in the middle of the document
>     >     and I want to jump somewhere else quickly (or even just go to the TOC).
>     >
>     >     It would be nice to have some sort of floating navigation bar containing
>     >     links to every section, rather than a TOC at the top. Failing that,
>     >     section numbers and hyperlinks to the top or end (a la
>     >     https://cran.r-project.org/doc/manuals/r-release/R-exts.html
>     <https://cran.r-project.org/doc/manuals/r-release/R-exts.html>
>      >     <https://cran.r-project.org/doc/manuals/r-release/R-exts.html
>     <https://cran.r-project.org/doc/manuals/r-release/R-exts.html>>)
>     would be
>      >     useful.
>      >
>      >     Cheers,
>      >
>      >     Aaron
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