An intro crash course for using R-markdown!
Feel free to post your questions in this Google Document!
Presentation Slides:
- IntroRMarkdown_NIAID_32421_PPT.zip [PowerPoint]
- IntroRMarkdown_NIAID_32421_PDF.zip [PDF]
Recommended Handouts: GitHub's Markdown Cheatsheet | R-Studio's RMarkdown Cheatsheet
Looking to the run examples on your own machine? First install R-studio and then the latest versions of the following packages:
dplyr
knitr
rmarkdown
flexdashboard
reticulate
plotly
kableExtra
leaflet
mapview
The following packages require a followup command to install software. These might need admin rights on your machine to install correctly!
webshot
<-- Installs PhantomJS - only needed if not already installed on machine
Then run in R: webshot::install_phantomjs()
tinytex
<-- Installs LaTeX - only needed if not already installed on machine
Then run in R: tinytex::install_tinytex()
On the R Studio Server - you can use the preinstalled packages by typing the following in the console:
old_path <- Sys.getenv("PATH")
Sys.setenv(PATH = paste(old_path, "/biocompace/bin", sep = ":"))
If you want to install the packages in your own local machine/directory, install the packages with the following line (and then run the install_tinytex
function above):
install.packages(c("dplyr","knitr","rmarkdown","kableExtra","flexdashboard","reticulate","plotly","leaflet","mapview"))
Note: If installing on your own machine, it might be easier on your machine to install LaTeX using a different installer rather than via TinyTex. See this page for more info!