Hi @afwhite! Welcome!
The best way to get help with your app is to create a small, self-contained reproducible example that others can run in order to understand your problem and work on solutions.
That can be hard with complicated data inputs, so before you even go that far, it might be worth first testing if this is even a Shiny-related problem. Are you able to plot these data the way you expect outside of your app, in a regular R script?