Question: Does BiocWorkflowTools package generate F1000Reseach/Bioconductor-stype PDF at once?
0
gravatar for Koki
11 months ago by
Koki0
Japan
Koki0 wrote:

Hi, 

I found that BiocWorkflowTools package can convert R markdown file to LaTex and PDF files, which is F1000Reseach-formatted.

http://bioconductor.org/packages/release/bioc/html/BiocWorkflowTools.html

I think the idea is amazing because the package will increase the value of Bioconductor's documents (vignette) as peer review papers.

However, I still do not clearly understand some parts, that is, the appearance of F1000-PDF and Bioconductor-PDF are different.

Is this F1000-PDF also can be used as Bioconductor's vignette, or this R markdown file can be converted to both F1000-PDF and Bioconductor-PDF/HTML for vignette, by some adjustment of the Rmd file such as change of header lines?

In my opinion, R-studio's knit botton that seamlessly switching F1000Research-pdf/Bioconductor-pdf or Bioconductor's acceptance of F1000Research-type vignette will reduce the burden of R-developers.

Off course, little rewriting the R markdown file is not so hard.

Thanks,

Koki Tsuyuzaki

ADD COMMENTlink modified 11 months ago • written 11 months ago by Koki0

From a Bioconductor stand point,  We encourage the use of BiocStyle but allow for other types of vignettes styles.  Using the F1000 Style for a vignette is already perfectly acceptable. 

ADD REPLYlink written 11 months ago by shepherl ♦♦ 1.4k
Answer: Does BiocWorkflowTools package generate F1000Reseach/Bioconductor-stype PDF at o
0
gravatar for Mike Smith
11 months ago by
Mike Smith3.5k
EMBL Heidelberg / de.NBI
Mike Smith3.5k wrote:

The original aim of the F1000 template was primarily to make writing and submitting workflow documents easier (https://www.bioconductor.org/developers/how-to/workflows/), where the intention is to send an F1000 style document to the journal, and have a BioC style HTML available via the Bioconductor website.  However there's no reason you can't use the F1000 styling for any R Markdown document, and as Lori says it acceptable, if not encourage, for package vignettes.


From a practical point of view, you can use both styles if by putting the following in the head of your R Markdown document:

output: 
    BiocStyle::html_document: default
    BiocWorkflowTools::f1000_article: default

If you're using the the 'knit' button in R Studio then I think it's only possible to produce the first entry, it doesn't let you select between the two. However, producing the output programmatically you can do any of the following:

## Output just Bioconductor style HTML
rmarkdown::render(input = "Document.Rmd", output_format = 'BiocStyle::html_document')
## Output just F1000Research style PDF
rmarkdown::render(input = "Document.Rmd", output_format = 'BiocWorkflowTools::f1000_article')
## Out both of the above
rmarkdown::render(input = "Document.Rmd", output_format = 'all')

That way you don't have to edit your document at all to produce the two formats, just change the argument to render()

Based on this, I guess there's no reason why both versions can't be made available on the BioC website, it might even be preferable for a reader to find a document that looks very similar to the published paper. This is probably something we need to think about.

ADD COMMENTlink modified 11 months ago • written 11 months ago by Mike Smith3.5k
1

Actually, RStudio GUI allows you to switch between the different output formats defined in the document's YAML header. You can select them from the dropdown list which can be expanded by clicking on the small arrow next to "Knit".

ADD REPLYlink written 11 months ago by Andrzej Oleś720
Answer: Does BiocWorkflowTools package generate F1000Reseach/Bioconductor-stype PDF at o
0
gravatar for Koki
11 months ago by
Koki0
Japan
Koki0 wrote:

Thanks, Lori and Mike!

I'll try the package.

ADD COMMENTlink written 11 months ago by Koki0
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