[Bioc-devel] minor suggestion for BiocStyle?

Thu Oct 2 22:42:46 CEST 2014

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).

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
>>>>>> 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
>>>>>>
>>>>>
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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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>>>> Phone: (206) 667-2793
>>>>
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>>>
>>>
>>
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>>
>
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-- 
Hervé Pagès

Program in Computational Biology
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