[Bioc-devel] improving navigation within workflows

[Andrzej Oleś]

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 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> 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
> >
> > On Sun, Jul 16, 2017 at 11:53 AM, Aaron Lun <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/>
> >
> >     ... 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>)
> would be
> >     useful.
> >
> >     Cheers,
> >
> >     Aaron
> >     _______________________________________________
> >     Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing
> list
> >     https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> >
> >
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