# [Bioc-devel] minor suggestion for BiocStyle?

Ramon Diaz-Uriarte rdiaz02 at gmail.com
Fri Oct 3 19:17:16 CEST 2014

```

On Thu, 02-10-2014, at 22:42, Hervé Pagès <hpages at fhcrc.org> wrote:
> Hi,
>
> This makes a lot of sense. I also find a bit disturbing that the main
> text cannot immediately be distinguished from other things like captions
> or page headers (BiocStyle places the title of the vignette at the top
> of each page but this header looks exactly like the main text, except
> that it's horizontally aligned with the page number at the top-right
> corner of the page).

Actually I am also disturbed by the way the page headers look. (But in
contrast to the suggestion for the float captions, I wasn't aware of a
quick fix).

Best,

R.

>
> Thanks,
> H.
>
> On 09/28/2014 06:59 AM, Kasper Daniel Hansen wrote:
>> 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
>>>>>>> Arzobispo Morcillo, 4
>>>>>>> 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
>>>>>>>
>>>>>>
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>>>>>>
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>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>>>> 1100 Fairview Ave. N.
>>>>> PO Box 19024 Seattle, WA 98109
>>>>>
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>>>>>
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>>>>
>>>>
>>>
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>>
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--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Arzobispo Morcillo, 4