Tutorial: BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
gravatar for Wolfgang Huber
26 days ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

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



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



ComplexHeatmaps, pheatmap


Venn diagrams



Caching  expensive computations or downloads

knitr ‘cache’ option for chunks     



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

learnr package by J.J.


Posters drposter


Books: bookdown



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?


ADD COMMENTlink written 26 days ago by Wolfgang Huber13k

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

ADD REPLYlink written 26 days ago by Johannes Rainer880
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