[Bioc-devel] minor suggestion for BiocStyle?

[Kasper Daniel Hansen]

I think it is very reasonable to be able to easily identify that something
is a caption as opposed to main text.  I have had this issue with floats in
vignettes before.  What is less clear to me (because I am not a designer)
is how to best achieve this.  It seems that we can use some (or all) of the
following
  - different margins
  - different font
  - different text size

I think Andrzej example looks decent (although I would also make the
margins a bit smaller), but I don't have any strong opinions about how to
reach the overall goal of making captions distinct.  I do strongly support
we do something though.

Best,
Kasper

On Sun, Sep 28, 2014 at 9:51 AM, Andrzej Oleś <andrzej.oles at gmail.com>
wrote:

> Dear all,
>
> please note that image captions in print (e.g. in journals like Nature,
> Bioinformatics, Genomics to name only a few) are often typeset with a
> slightly different, typically smaller font size. This makes them visually
> distinct from the main paragraph text and gives more overall structure to
> the document. It makes a difference especially in case of long multi-line
> captions.
>
> To give you an idea how a BiocStyle document with captions typeset with
> smaller font and with boldface label would look like I attach the modified
> DESeq2 vignette. Please compare with the regular one in devel.
>
> Cheers,
> Andrzej
>
> On Sun, Sep 28, 2014 at 10:37 AM, Wolfgang Huber <whuber at embl.de> wrote:
>
> >
> > AfaIcs everybody (incl. myself) involved in this so far is an amateur
> when
> > it comes to graphics design and text layout.
> > This not to minimize the technical achievement!
> > Anyway, input from someone with graphics design / text layout credentials
> > (also privately) is welcome.
> >
> >         Wolfgang
> >
> > Il giorno 28 Sep 2014, alle ore 00:52, Martin Morgan <mtmorgan at fhcrc.org
> >
> > ha scritto:
> >
> > > On 09/27/2014 10:01 AM, Andrzej Oleś wrote:
> > >> Hi Ramon,
> > >>
> > >> many thanks for your feedback an for your nice suggestion! Having more
> > >> distinctive image captions is for sure something worth considering. I
> > >> personally like the idea of having them typeset in a slightly smaller
> > font
> > >> and with boldface label. Additional margin seems reasonable as well.
> I'm
> > >> not sure about changing the label separator, though.
> > >>
> > >> If there are no objections I would be happy to incorporate this into
> > >> BiocStyle.
> > >
> > >
> > > Because
> > >
> > > - It seems very easy for one style to conflict with another in LaTeX
> > >
> > > - It's 'easy' (in the LaTeX sense of the word!) for the user to add
> > their own customizations.
> > >
> > > - Style is quite a personal thing
> > >
> > > I'm not (without having looked at the changes!) in favor of this.
> > >
> > > Martin
> > >
> > >
> > >>
> > >> Best,
> > >> Andrzej
> > >>
> > >> On Sat, Sep 27, 2014 at 8:51 AM, Ramon Diaz-Uriarte <
> rdiaz02 at gmail.com>
> > >> wrote:
> > >>
> > >>> Dear All,
> > >>>
> > >>> I am now using BiocStyle for most of the latex I produce (even
> non-bioc
> > >>> related, such as teaching class notes) but I find that the text of
> the
> > >>> caption is often not distinct enough from the rest of the surrounding
> > text,
> > >>> especially with multi-line captions.
> > >>>
> > >>> I fix that using the caption package, with options
> > >>>
> > >>> \usepackage[margin=10pt,font=small,labelfont=bf,
> > >>> labelsep=endash]{caption}
> > >>>
> > >>>
> > >>> (directly from p. 4 of the documentation).
> > >>>
> > >>>
> > >>> I wonder if it might be worth to make something like this the
> default.
> > (And
> > >>> I of course understand that this falls under "highly subjective
> choice
> > and
> > >>> thus user customization" and is up to us to do it if we want, so
> > disregard
> > >>> if irrelevant).
> > >>>
> > >>>
> > >>> Best,
> > >>>
> > >>>
> > >>> R.
> > >>>
> > >>> --
> > >>> Ramon Diaz-Uriarte
> > >>> Department of Biochemistry, Lab B-25
> > >>> Facultad de Medicina
> > >>> Universidad Autónoma de Madrid
> > >>> Arzobispo Morcillo, 4
> > >>> 28029 Madrid
> > >>> Spain
> > >>>
> > >>> Phone: +34-91-497-2412
> > >>>
> > >>> Email: rdiaz02 at gmail.com
> > >>>        ramon.diaz at iib.uam.es
> > >>>
> > >>> http://ligarto.org/rdiaz
> > >>>
> > >>> _______________________________________________
> > >>> Bioc-devel at r-project.org mailing list
> > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>>
> > >>
> > >>      [[alternative HTML version deleted]]
> > >>
> > >> _______________________________________________
> > >> Bioc-devel at r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>
> > >
> > >
> > > --
> > > Computational Biology / Fred Hutchinson Cancer Research Center
> > > 1100 Fairview Ave. N.
> > > PO Box 19024 Seattle, WA 98109
> > >
> > > Location: Arnold Building M1 B861
> > > Phone: (206) 667-2793
> > >
> > > _______________________________________________
> > > Bioc-devel at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
>
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