[Bioc-devel] BiocStyle and R markdown

[Thomas Girke]

Perfect, if your update in Bioc-devel eliminates the awkward bullets in
front of the numbers. The lack of numbered content tables in Bioc-release
may be something we have to live with until the next Bioc release? I don't
want to overstretch Dan's or the Bioc team's patience with overly picky
style requests.
Thomas

On Wed, Jul 29, 2015 at 6:49 PM Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:

>  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
>>>
>>

	[[alternative HTML version deleted]]