Tutorial: BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
gravatar for Wolfgang Huber
2.4 years 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.



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


biocstyle tutorial rmarkdown • 1.4k views
ADD COMMENTlink written 2.4 years 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 2.4 years ago by Johannes Rainer1.5k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 366 users visited in the last hour