Chapter 10 Slide deck component

Powered by reveal.js, the online slide deck is an R markdown template utilized by RNASequest to generate an interactive slide deck with emphasis on the graphical representation of QC and basic analysis plots, which makes the primary analysis presentation-ready for engaging biologists to discuss the initial results immediately. Again, it is also GitHub-friendly in terms of hosting.

Please visit an example of the online slide deck using the following link:

https://interactivereport.github.io/RNASequest/ShinyOne/SRP199678/SlideDeck/index.html

Here is the tutorial to create your own slide deck after running the EA pipeline:

1, Find the path of the bookdown.info.txt file, it is located in:

***/YourPorjectName/EA******/BookdownReport/bookdown.info.txt

2, Go to the RNASequest/src dir, and modify line #29 of script ‘Slidedeck.Rmd’:

info_txt <- <your bookdown.info.txt path>

3, Finally render the slide deck:

The slide deck Slidedeck.Rmd script is under the /src directory of the RNASequest installation.

Rscript -e 'rmarkdown::render("~/RNASequest/src/Slidedeck.Rmd", output_file="yourslidedeck_name.html")'

Then it will generate yourslidedeck_name.html for visualization.

Please note:

1, Please run EAreport first before generating the slide deck. For more details, please check the manual.

2, The Slidedeck.Rmd only plots the first two covariates for ‘covariates plot’, so as to avoid plotting hundreds of figures/slides. If users want to plot a specific covariate, please edit the ‘config.yml’ file by moving your desired covariates to the first two.

For example:

# The original:
covariates_check: [cvt1, cvt2, …, cv_desire1, cv_desire2, …]

# Change it to:
covariates_check: [cv_desire1, cv_desire2, cvt1, cvt2, …]