[Bioc-devel] BiocStyle and R markdown

[Kasper Daniel Hansen]

When I roll that styles.css into the bioconductor.css file shipping with
BiocStyle, it gets rid of the bullets.

Its added to BiocStyle 1.7.5

Kasper

On Wed, Jul 29, 2015 at 9:37 PM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:

> This is just reporting what I see using Bioc-devel:
>
> I get a TOC where each line looks like
>
>   <BULLET> <SECTION_NUMBER_AS_LINK> <SECTION_TITLE_AS_LINK>
>
> While I agree that the bullet is kind of ugly (and would be great to get
> rid of), I do get the section numbering functionality you want.
>
> Note: for this report I am rendering the Rmd file myself, I haven't tested
> how it looks when I do it as a vignette.
>
> It would be great to expand on the BiocStyle vignette and discuss
> citations and other issues and also include a clear template file.  I am
> planning on doing some pull request along those lines soon; I have been
> testing Rmd -> HTML extensively for a course I am developing, but I am also
> new to the knitr+markdown thing so I am still experimenting.
>
> Kasper
>
>
> On Wed, Jul 29, 2015 at 4:44 PM, Thomas Girke <thomas.girke at ucr.edu>
> wrote:
>
>> A simple formatting issue:
>>
>> Since support for table of contents in R markdown vignettes has become
>> available, it seems like an amazing solution for many online
>> documentation needs in the future.
>>
>> What would help me to fully to adopt to it, is a solution to get rid of
>> the bullets in a numbered table of content which looks a bit unusual to
>> me:
>>
>> http://www.bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
>> For navigating longer documents numbered tables of contents are an
>> essential feature to me, which I believe wasn't available in earlier R
>> markdown versions or sometimes they showed up in unacceptable places
>> like before the title of a document.
>>
>> A prescribed solution to get rid of these bullets from here
>>
>> http://stackoverflow.com/questions/28138456/rmarkdown-with-knitr-to-html-how-to-hide-bullets-in-toc-table-of-contents
>> didn't work for me.
>>
>> Also, it would be nice to be able to generate the exact same vignette
>> style in Bioc release and development, but it seems others have
>> difficulties with this too, probably due to version differences of R
>> markdown as seen here:
>>
>> http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
>>
>> Thanks for making BiocStyle and R markdown available. I really enjoy
>> using them. The resulting HTML pages look professionally designed and
>> are highly functional while allowing us to focus on generating content
>> in a consistent format rather than getting lost in formatting issues.
>>
>> Thomas
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

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