Made a prototype RShiny app that reads results and makes a volcano plot. But it is not very good right now.
It needs a way for users to select the comparison to show. Also, it puts all the SL4 and SL5 genes onto the same plot, which is weird.
It might be better to show two plots - SL4 and SL5 next to each other.
Finally, an RShiny app showing just one or two plots makes it difficult to quickly assess all the results. I bet it would be better to write a Markdown that creates all the plots and then just puts them into a multipage PDF, like we did with this paper ages ago: https://pubmed.ncbi.nlm.nih.gov/17369640/

Unfortunately, however, I can't find the multi-page PDF *or* the code!

branch:

https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3479

cc: [~molly]

More details on what this task involves:

• Make a new Markdown that uses code from "DrawPlots.R" to create an HTML or PDF Markdown output file that shows volcano plots for every comparison shown in 72_F3H_PollenTube/results/MvW-SL4.txt and 72_F3H_PollenTube/results/MvW-SL5.txt

Merged RShiny app code and new DrawPlots.R into main branch. Proceeding with new Markdown to create volcano plots in "bulk".