Tutorial:BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
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@wolfgang-huber-3550
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EMBL European Molecular Biology Laborat…

Here's a few notes from the birds of a feather session at the Bioconductor Developer Day 2017-07-26

Writing papers in Rmarkdown, BiocStyle... (and books, posters)

 

Multi-panel figures

CRAN package multipanelfigure

 

Tables

knitr:  kable (ideally if you then also define your own CSS); xtable

interactive tables: DT CRAN package, an interface to JavaScript DT

see example in glimma

Titles and captions? pass to kable, and use HTML-style

tables package

 

Heatmaps

ComplexHeatmaps, pheatmap

 

Venn diagrams

upsetR

 

Caching  expensive computations or downloads

knitr ‘cache’ option for chunks     

BiocFileCache

 

Color palettes for figures

Rcolorbrewer; ggplot2 defaults; viridis, ggthemes, wesanderson, cardigans, dill/beyonce (github)

 

Convert from markdown to word:  pandoc

 

Bibliography styles for various journals:

rticles package:  by RStudio, and for their types of journals; community input for more styles? (should we care about proliferation of arcane citation ‘standards’?)

 

Authoring tutorials

http://swirlstats.com/

learnr package by J.J.

 

Posters

https://github.com/bbucior/drposter drposter

 

Books: bookdown

 

WIshlist:

Infinite scrolling, e.g. for reading on tablets

Track changes functionality?

 

For non-technical collaborators:

  • How to annotate comments in the rendered PDF or HTML file and feed them back into the source: github?  There is a (are) JavaScript library(ies) that can annotate rendered HTML pages

  • How to make changes on the rendered HTML and then feed them back?


 

biocstyle Rmarkdown Tutorial • 1.7k views
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Regarding tables for markdown (and other): I'm using the pander package (with the pandoc.table function), which supports also captions/titles.

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