[Bioc-devel] minor suggestion for BiocStyle?

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 Ole? <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 Ole? 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 Aut?noma 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

      [[alternative HTML version deleted]]

--
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

	[[alternative HTML version deleted]]