Generally speaking, R code that works on some other machine should work when executed as a script from within LabKey Server.

Are you getting any error messages? It's possible that the server is missing a required library that's already been installed on the machine where you're running the R code stand-alone. I've also seen some minor differences in R chart outputs on different platforms (Windows vs Linux, for example), mostly around font sizing and rendering. Are you running on the same operating system in both places?

Thanks,
Josh