[Bioc-devel] Vignettes with many output graphics - How to fulfill the Bioc build requirements, best practises?

[Kasper Daniel Hansen]

Another alternative to this is the following hack. If you function foo()
produces "tons of output" is it possible to add an argument like
  foo(data, plot_number = 4)
to selectively plot something. This argument would not really be intended
for end-users, and it would have a default of (say) plot_number = NULL
meaning all pages are produced. This was you can selectively plot things
for you vignette, and this may not be too hard to add, for example if your
many plots are being produced by a for loop or similar.

Best,
Kaspr

On Tue, Mar 22, 2022 at 4:37 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> Yes, moving the heavy vignette to a workflow package is probably a good
> idea. See this post from last month for more info about workflow packages:
>
> https://stat.ethz.ch/pipermail/bioc-devel/2022-February/018821.html
>
> Cheers,
>
> H.
>
>
> On 22/03/2022 13:09, Marcel Ramos wrote:
> > Hi Christian,
> >
> > Thanks for reaching out.
> >
> >   From what I gather, perhaps a workflow package submission is more
> > appropriate for the
> > details that you would like to submit within the vignette. We recommend
> > vignettes that have
> > small and run-able examples (possibly from simulated data) that
> > demonstrate package functionality.
> >
> > I haven't taken a look at the 'mysterious' package but perhaps consider
> > breaking up the functionality
> > into separate packages, if possible. For example, you could have one
> > package for each of the facilities
> > (e.g., stats, viz, utils, etc).
> >
> > As for producing PDFs from plotting functions, this is generally
> > discouraged.
> > Plotting functions should work like plot(1:10) and should output a
> > single plot (or grouped plots)
> > to the graphics device. The user should then be free to choose the file
> > format for any plot produced.
> > This approach may in turn resolve the issues you describe with plots in
> > the vignette.
> >
> > It may require some time re-designing the package(s) but I think your
> > users would benefit
> > in the long run.
> >
> > Best regards,
> >
> > Marcel
> >
> > On 3/22/22 4:05 PM, James W. MacDonald wrote:
> >> If the pages from the PDF are essentially static (for your vignette,
> that is), why not run it once, get the pngs, save them somewhere, and use
> eval = FALSE in the knitr headers for the plot* fuctions. Then you will
> speed things up, there won't be all this extra PDF documentation that's +/-
> not part of the vignette, and it should run much faster.
> >>
> >> -----Original Message-----
> >> From: Bioc-devel<bioc-devel-bounces using r-project.org>  On Behalf Of
> Christian Arnold
> >> Sent: Tuesday, March 22, 2022 3:33 PM
> >> To:bioc-devel using r-project.org
> >> Subject: [Bioc-devel] Vignettes with many output graphics - How to
> fulfill the Bioc build requirements, best practises?
> >>
> >> Hi, I wanted to reach out for some thoughts on the following problem I
> am facing with a package I recently submitted to Bioc. In essence, I am
> struggling with the 15 minutes time limit for R CMD check as well as the
> package size limit of 5 MB. The latter is more important, so let's focus on
> that:
> >>
> >> It is a quite large package with many functions, a full workflow for
> building gene-regulatory networks, and we want to include a detailed
> workflow vignette where the most important output plots are shown and
> explained, to make it user-friendly and easy to apply.
> >>
> >> For various plot* functions produce PDFs that have many pages
> (sometimes dozens or even hundreds), only some of which should be shown in
> the vignette (say page 2 and 5 from PDF A, and page 1 and 2 from PDF B,
> etc). Including selected pages from a PDF doesnt seem to be possible with
> BiocStyle (please correct me if I am wrong), so currently, I am
> automatically converting each page of each of the various PDFs as a png
> image, to include selected pages then in the Vignette via
> knitr::include_graphics. This works well, but leads to the repo being too
> big (currently 11 MB) when being build - because the original images as
> well as the resulting htmls in the inst folder contain the images, making
> it bigger than 5 MB. I could reduce the resolution of the images much
> further, but this feels wrong also. In total, we talk about 40 or so images
> that I wanted to share across the different vignettes.
> >>
> >> Are there any thoughts on how I can proceed here without spending a lot
> of time on re-designing the package logic (which I unfortunately dont have
> at this point) and without sacrificing the usability of the package (I
> could just remove the Workflow vignette or host it externally I guess)?
> >>
> >>
> >> Thanks, your input is very appreciated.
> >>
> >>
> >> Best
> >>
> >> Christian
> >>
> >> _______________________________________________
> >> Bioc-devel using r-project.org  mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >> _______________________________________________
> >> Bioc-devel using r-project.org  mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > ---
> > Marcel Ramos
> > Bioconductor Core Team
> > Roswell Park Comprehensive Cancer Center
> > Dept. of Biostatistics & Bioinformatics
> > Elm St. & Carlton St.
> > Buffalo, New York 14263
> >
> >
> > This email message may contain legally privileged and/or...{{dropped:4}}
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Best,
Kasper

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