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 <a...@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 <a...@wehi.edu.au > > <mailto:a...@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@r-project.org <mailto:Bioc-devel@r-project.org> mailing > list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
