# p5

w and s move the left paddle, o and l move the right paddle.

# R Markdown

This post is written as a .Rmd file. Regular R code works.

Test:

knitr::include_url("/slides/dataintro19")

However, a number of workarounds are necessary to fix the dependency problems between the hugo academic theme, R markdown, DT, plotly and mermaid (the latter two being html widgets).

# Tests

## DT

Getting DT to work properly requires the steps performed to close this issue: https://github.com/dcossyleon/blogdown_desiree/issues/1

DT::datatable(head(iris))

I still need to make it work properly with the dark mode of this theme.

## Plotly

A regular ggplot renders just fine. But a plotly graph of said ggplot object Will not be displayed until you set math = false in the configuration file params.toml. This is due to a clash of mathJax versions in plotly, rmarkdown and the hugo academic theme.

print("test")
## [1] "test"
plt <- ggplot2::ggplot(ggplot2::mpg, ggplot2::aes(displ, cty)) +
ggplot2::geom_point()
plotly::ggplotly(plt)

However, while this options brings back plotly, it also disables math rendering for this document on the site.

### Bringing back the Math

We can somewhat hackily circumvent this by including our own mathJax in the sites JS dependencies. To do this, leave academics math option disabled (=false), open up layouts/partials/site_js.html (you should have this from the DT fix linked to in the first section of this post) and add these lines near the top:

{{/* We load our own mathJax here, some html widgets seem to need it loaded first */}}
<script src="//yihui.org/js/math-code.js"></script>
<script async
src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML">
</script>

This solution is inspired by https://bookdown.org/yihui/blogdown/templates.html. The CDN used here is the link that bookdown html books use and I found it in the html source of a book I have on my website while searching a files for mathJax.

$sd = \sqrt{\frac{\sum_{i=0}^{n}{(x_i-\bar x)^2}}{(n-1)} }$

## diagrammeR

The current version of mermaid has some unfortunate css scoping issues that clash with R markdown documents in general. To fix those, go to your R library path and find the DiagrammeR package. Then modify \$HOME/R/x86_64-pc-linux-gnu-library/3.6/DiagrammeR/htmlwidgets/lib/mermaid/dist/mermaid.css

and replace every .section with .DiagrammeR .section.

Restart R to reload the library.

DiagrammeR::mermaid(
"
graph TB
A-->B
A-->C
C-->E
B-->D
C-->D
D-->F
E-->F
")

Before this fix, mermaid.css would basically grey out your whole page.

I do love the academic theme, but in the long run I might consider switching to a more lightweight theme, as most features introduced by academic where already covered by Rmarkdown / blogdown and will inevitably lead to clashes.

###### Biochemist / Bioinformatician

Biochemistry Master student at Heidelberg University