See linked ticket for comments on barplot app. We created it (initially) as a proof-of-concept for the linked ticket.

For review, see comment from linked ticket, copied here:

Hi Molly Davis!

I am pushing a new branch to my fork with my barplot code.

A couple of changes:

The new code supports both SL4 and SL5.
I changed the y axis label to include the string "(scaled counts)"
See:

https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3449-1

Note that because the above work started as part of a different ticket, the branch name uses the name of the other ticket instead of this one.

Review:

• I ran the app on my computer and it works perfectly with SL4 and SL5 genes.
• Only comment is we might want to name our app scripts differently if we are going to add multiple to the repo.

Ready for PR!

I am going to rename the app to avoid name conflict and then submit a PR.

Changes:

• Changed branch name to match this ticket: https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3481
• Renamed app.R to BarplotApp.R to avoid conflicts with other apps under development and for clarity

PR submitted and merged into main. Ready for testing.

Testing:

• Running the app on my machine and had no issues with it launching
• SL4 and SL5 gene names both work now with the app
• I did run into an error under certain conditions. If the SL5 gene name has NA as the description it throws this error: missing value where TRUE/FALSE needed. Might need to add code that deals with this occurrence and fill the title with something else like "Unknown protein" or something like that.

Moving back to To Do!

Fixed the bug. Tested a gene Solyc10G001086 that has "NA".
Also, added more info the display. Now it says what genome assembly the gene came from.
Redeployed to https://ann-loraine-gmail.shinyapps.io/barplot/

Tested the new redeployed app and the error is gone! Thank you!

Moving to done!