Mind -> blown. Yes, that's exactly what I wanted, thanks. -Aaron
On 04/08/17 14:19, Andrzej Oleś wrote: > Hi Aaron, > > I'm happy to inform that I've implemented your suggestion to add > navigation links at workflow pages. Feel free to have a look at the > working prototype under > https://www.bioconductor.org/help/workflows/testproj/testfile/ > > The new workflow-rendering engine which includes the navigation links > will be enabled soon after some additional testing is finished. The > transition will be announced in a separate email to the devel mailing list. > > Cheers, > Andrzej > > > On Mon, Jul 17, 2017 at 10:15 AM, Aaron Lun <a...@wehi.edu.au > <mailto:a...@wehi.edu.au>> wrote: > > 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/ > <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> > > <http://bioconductor.org> website template. Links to the TOC, such as > > ones in e.g. > > https://www.bioconductor.org/help/workflows/highthroughputassays > <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 > <mailto:a...@wehi.edu.au> > > <mailto:a...@wehi.edu.au <mailto: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 > > <http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html> > > > <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 <a...@wehi.edu.au > <mailto:a...@wehi.edu.au> <mailto:a...@wehi.edu.au > <mailto:a...@wehi.edu.au>> > > > <mailto:a...@wehi.edu.au <mailto:a...@wehi.edu.au> > <mailto: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/> > > > <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/> > > > <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>> > > > > <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 > > > _______________________________________________ > > > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > <mailto:Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>> > > <mailto:Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org> <mailto: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> > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> > > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>>> > > > > > > > > _______________________________________________ > > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > <mailto: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> > > <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
