Does BiocWorkflowTools package generate F1000Reseach/Bioconductor-stype PDF at once?
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Koki ▴ 10
@koki-7888
Last seen 4 months ago
Japan

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

workflows biocworkflowtools bioconductor • 831 views
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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.

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Mike Smith ★ 5.6k
@mike-smith
Last seen 21 hours ago
EMBL Heidelberg / de.NBI

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.

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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".

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Koki ▴ 10
@koki-7888
Last seen 4 months ago
Japan

Thanks, Lori and Mike!

I'll try the package.